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caTIES Training – Day 1 Duration : 3 Hours

caTIES Training – Day 1 Duration : 3 Hours. Girish Chavan. Training Schedule. Researcher Training Introduction to caTIES Searching for reports. Viewing results. Honest Broker & Administrator Training Introduction to user roles, distribution protocols, ordering.

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caTIES Training – Day 1 Duration : 3 Hours

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  1. caTIES Training – Day 1Duration : 3 Hours Girish Chavan

  2. Training Schedule Researcher Training • Introduction to caTIES • Searching for reports. • Viewing results. Honest Broker & Administrator Training • Introduction to user roles, distribution protocols, ordering. • Ordering tissue as a researcher. • Honest Broker functions in caTIES. • Introduction to users, organizations, and distribution protocols. • Administrator functions in caTIES.

  3. Schedule • Introduction to caTIES • Logging into caTIES • caTIES Researcher Perspective • Dashboard query builder • Diagram query builder • Saving / loading queries

  4. What is caTIES? Stands for? cancer Text Information Extraction System Which text? Pathology reports from coPath. What information? Medical concepts, negation What else? Search this information, order tissue, support honest broker services

  5. Some key features • De-identification • Access from anywhere. • Concept based queries • Temporal queries. • Search multiple organizations • Honest broker support • Role based access.

  6. caTIES User Roles Researcher Can search path reports and create orders Honest Broker Can search path reports and process orders Administrator Can create new users, protocols and assign roles

  7. Schedule • Introduction to caTIES • Logging into caTIES • caTIES Researcher Perspective • Dashboard query builder • Diagram query builder • Saving / loading queries

  8. Minimum Requirements • Windows XP/2000 • Java 1.5+Download latest version at http://www.java.com

  9. Link to the caTIES Client The caTIES client is served as a Java Webstart application Click below to access the client: http://www.caties.cabig.upmc.edu/caties_3_0/ This will open up a Java webstart window that will download the caTIES application to your computer. This will take a while, fortunately this happens only the first time you are accessing caTIES. After Webstart has finished downloading it, the caTIES Login prompt will be displayed.

  10. Logging into caTIES 1: Select ‘Local Test CTRM’ from the drop down box and then click the OK button The CTRM ( Collaborative Tissue Resource Manager ) is the server that maintains user accounts. Typically there is a separate CTRM for testing and demo purposes that uses dummy data.

  11. Logging into caTIES 2: Enter your username and password and click then click the Login button Logging in takes typically 1 to 3 minutes.

  12. Logging into caTIES 3: Select ‘Researcher’ as the role from the first drop down box, and select ‘caTIES Training -1’ as the initial distribution protocol from the second box. Click on OK to finish the logging in process.

  13. Schedule • Introduction to caTIES • Logging into caTIES • Researcher Perspective • Dashboard query builder • Diagram query builder • Saving / loading queries

  14. Researcher Perspective Buttons for new, open and save query Minimize query builder to give more space to results pane Switch query builders Search button Results Pane Query Builder Pane Adjust width of panes by dragging grey space between panes

  15. Researcher Perspective • Used to create, open and save and run queries. • Used to browse results and create case sets. • Used to create, modify and submit tissue/data requests.

  16. Schedule • Introduction to caTIES • Logging into caTIES • Researcher Perspective • Dashboard query builder • Diagram query builder • Browsing the results • Saving / loading queries

  17. Simple Dashboard The simple dashboard text box works very much like a Google™ search bar. It is designed for very basic queries like: “Get me reports with adenocarcinoma” caTIES selects the best matching metathesaurus concept for each search term entered, and returns the reports that containing the concept. If there are multiple search terms, the reports returned contain all of the matching concepts. To switch to the Advanced Dashboard Enter search terms here.

  18. Simple Dashboard Exercises Queries with a single word search term Problem: Get me reports with adenocarcinoma. STEP 1: Enter ‘adenocarcinoma’ in the search box. STEP 2: Click on ‘Start Search’ button. STEP 1 STEP 2

  19. Browsing the results Query status Maximize query builder Search within the results table. Results in tree format. Grouped by owning org. and patient. Select any report in the tree to view it. Results in tabular format. Sort by any column by clicking on column name. Double click on any row to view that report.

  20. Report View You can add this report to an order here. You can also print the report text and access quality assurance features. De-identified report text. You can view the annotations and search terms by using the radio buttons. Double clicking on an annotation will display that concept entry on the NCI Metathesaurus website.

  21. Concept Search vs. Text Search • Treating search terms as Concepts generally returns more accurate results. • Concept search returns reports containing the search term, as well as reports containing the synonyms of the search term. For example, when searching for reports containing ‘Bronchiolitis Obliterans Organizing Pneumonia’, text search will only return reports containing exactly that string whereas concept search will additionally return reports containing BOOP, COP, and any other synonyms of BOOP. • Search terms entered in the NOT box (last search box) should be absent from the report text when doing text search, whereas they need to be presented in the negated form within the report, when performing a concept search. For example, if you enter ‘Adenocarcinoma’ in the NOT box, and do a text search, it will return all reports not containing the word ‘Adenocarcinoma’, whereas if you do a concept search, it will only return reports containing phrases such as ‘No evidence of adenocarcinoma’ or ‘Adenocarcinoma not found’.

  22. Simple Dashboard Exercises Queries with a multi-word search term Problem: “ Get me reports with atypical ductal hyperplasia” STEP 1: Since ‘atypical ductal hyperplasia’ is one concept, we indicate this by grouping the multiple words together by enclosing them in quotes. Enter “atypical ductal hyperplasia” in the search box (with quotes) STEP 2: Click on ‘Start Search’ button. STEP 1 STEP 2

  23. Simple Dashboard Exercises Queries with multiple concepts Problem: “ Get me reports with biopsies indicating atypical ductal hyperplasia” STEP 1: Enter “atypical ductal hyperplasia” in the search box (with quotes) followed by ‘biopsy’ (without quotes) STEP 2: Click on ‘Start Search’ button. STEP 1 STEP 2

  24. Switching to Advanced Dashboard For more advanced queries that let you specify demographic constraints or use boolean logic, we need to use the Advanced Dashboard. To switch to the ‘Advanced Dashboard’ click on the ‘More search options’ button. To switch to the Advanced Dashboard

  25. Advanced Dashboard The Advanced Dashboard is always synced with the Simple Dashboard, so if you had a query already entered in the Simple Dashboard, it will be copied over to the Advanced Dashboard. Select ‘Concept’ to map the search terms to metathesaurus concepts and search with those concepts. Select ‘text’ to treat the search terms as text strings. This box is the same as Simple Dashboard box. Additional search boxes that let you specify boolean OR and NOT logic. Specify demographic criteria for the patient here To switch back to the Basic Dashboard

  26. Advanced Dashboard Exercises Query with demographic criteria Problem: Search for 30-40 yr old females with ‘Bronchiolitis Obliterans Organizing Pneumonia’ ( BOOP ) STEP 1: Enter BOOP in the first search box. STEP 2: Since we want to specify an age range, Click on the ‘ranging between’ radio button in the Age box. STEP 3: Enter 30 in the min box and 40 in the max box. STEP 4: Select ‘Female Gender’ in the Sex box. STEP 5: Click on ‘Start Search’ button. STEP 1 STEP 2 STEP 5 STEP 3 STEP 4

  27. Advanced Dashboard Exercises Query with OR Problem: Search for reports with ‘cicatrix’ or ‘radial scar’ STEP 1: Since we want either of the terms to be present in the report, we will use the second search box. Enter “cicatrix” and “radial scar” in the second search box. STEP 2: Click on ‘Start Search’ button. STEP 1 STEP 2

  28. Advanced Dashboard Exercises Query with NOT Problem: Search for reports with ‘endobronchial lipoma’ but no ‘adenocarcinoma’ STEP 1: Enter “endobronchial lipoma” in the first search box STEP 2: For NOT, we use the last search box. Concepts in this box must be explicitly negated in the matching reports. For e.g. ‘no evidence of adenocarcinoma’ is a negated form of ‘adenocarcinoma’Enter ‘adenocarcinoma’ in the last search box. STEP 3: Click on ‘Start Search’ button. STEP 1 STEP 2 STEP 3

  29. Schedule • Introduction to caTIES • Logging into caTIES • Researcher Perspective • Dashboard query builder • Diagram query builder • Saving / loading queries

  30. Diagram Query Builder Diagram Query Builder is used to model complex boolean queries and temporal queries. Diagram button Control panel to edit diagram. The diagram can also be edited using the mouse. Initial diagram with a single search term box

  31. Diagram Components • A query diagram consists of boxes connected by arrows. • A box in the diagram view is used to represent a filter constraint on the query. The arrows indicate the order in which the various constraints are checked on any report. • The start and end placeholders are special boxes that represent the start and end of the diagram. • One can imagine the diagram as a river of pathology reports flowing from the Start Placeholder to the End Placeholder along the arrows connecting the different boxes. The boxes or filters that the river encounters in its path, filter out reports, and allow the rest of the reports to flow out. The result of the query are all the reports that make it to the End Placeholder. • Forks in the path of the river indicate boolean OR conditions. • Filters on the same path are logically ANDed together.

  32. Constraint Box Types • Search Term • NOT Search Term • Age • Sex • Race

  33. Interacting with the diagram • Right clicking on any part of the diagram will display a context sensitive menu that will let you add/remove filter constraint, modify constraint properties or add/remove temporal sub-queries. The menu option will differ based on what was right clicked. • All elements in the diagram can be moved around by selecting them and dragging the mouse pointer. • You can resize any box by dragging any of the 8 small squares displayed around it when it is selected. • You can delete any box (except the Start and End placeholders) by selecting it and pressing the ‘Delete’ key on the keyboard or by right-clicking on the box and selecting ‘Delete Constraint’ from the popup menu.

  34. Interacting with the diagram • Using the control panel • Steps: • First you need to select a reference box in the diagram. For a new query this can be either the Start or End placeholder. You can select a box by left-clicking on it until the small squares are displayed around its border. • Select the boolean operator to be applied between the reference box and the new constraint. If you selected AND, you need to specify whether you want the new constraint above or below the reference box. For OR, this is not required. • Select the constraint type for the box. The NOT checkbox is enabled only for ‘Search Term’ constraint type. Check it to specify negated or NOT boolean operation on search terms. • Click on the ‘Insert Constraint’ button to finish. • NOTE: Everything that you can do with the control panel can be done using the context sensitive menus displayed when you right-click on the diagram’s elements. STEP 4 STEP 3 STEP 2 STEP 1

  35. Diagram Modeler Exercises Query requiring Boolean AND Problem: “Get me reports with biopsies indicating atypical hyperplasia” STEP 1: By default the diagram modeler adds a search term box between the start and end placeholders when a new query is created. We can reuse this box for one of the search terms. If it does not exist, you can add one by right-clicking the arrow between the start and end placeholders and selecting ‘Add ANDed Constraint’ from the menu. You can also use the ‘Insert Constraint’ button to do the same thing. We will use this when we add the box for ‘biopsy’. Double-click on the search term box to modify its constraints. This will open a new dialog box titled ‘Specify Search Term’. STEP 2: Enter ‘atypical hyperplasia’ in the text box beside the ‘Concept’ button. STEP 3: We want to do a concept search so click on the ‘Concept’ button. caTIES will now search the NCI Metathesaurus for ‘atypical hyperplasia’ and show the results in a new window. continued on next slide… STEP 1 STEP 2 STEP 3

  36. Diagram Modeler Exercises STEP 4: From the search results displayed, select the best matching concept. You can double click on the concept name to see the description of the concept in the NCI Metathesaurus website.You can select multiple concepts if you feel they are both good matches. When multiple concepts are added to a single box, they are ORed together. STEP 5: Click on ‘Add Concept’ button to add it as a concept to your search term box. This will also close the Metathesaurus search window. Tip: You may also drag and drop the selection into the dialog box on the left to add it. STEP 6: Click on OK button to finish modifying the constraint box. You will see the concept added in the box. continued on next slide… STEP 4 STEP 5 STEP 6

  37. Diagram Modeler Exercises STEP 7: Now to add constraint box for biopsy we will use the control panel on the top of the diagram. See this slide to understand how the control panel works. Select the search term box with ‘Atypical ductal…’ concept within it. This will be our reference box. STEP 8: Select the ‘AND’ as the operator and ‘Below’ as the position from the control panel. STEP 9: Select ‘Search Term’ as the constraint type from the drop down box. STEP 10: Click on ‘Insert Constraint’ to add the box below our reference box. This will add a box to the diagram and automatically popup the Specify ‘Search Term’ box that will let you modify the constraint properties for the newly added box. continued on next slide… STEP 9 STEP 10 STEP 8 STEP 7

  38. Diagram Modeler Exercises STEP 11: Similar to how we added a concept for “atypical ductal hyperplasia” we need to add a concept for biopsy. Repeat steps 2-6, this time for‘biopsy’ . Your final diagram should look like this: STEP 12: That’s it. Click on Start Search button to run the query

  39. Diagram Modeler Exercises Query with Boolean OR Problem: Search for reports with either lobular carcinoma in situ with microcalcifications in the breast or, hepatocellular carcinoma with liver cirrhosis STEP 1: Just like in the exercise for Boolean AND, we will reuse the empty search term box that is added when a new query is created. Modify its properties to add ‘lobular carcinoma in situ’ as a concept to it. In the diagram we have resized the box to view the complete labels. STEP 2: To add ‘hepatocellular carcinoma’, with an OR relationship with ‘lobular carcinoma in situ’ we will select the ‘lobular carcinoma in situ’ box as the reference box. STEP 3: Select ‘OR’ as the operator in the control panel. STEP 4: Select ‘Search Term’ as the constraint type. STEP 5: Click ‘Insert Constraint’ button to add it to the diagram. This should also automatically popup the Specify Search Term dialog box. continued on next slide… STEP 4 STEP 5 STEP 3 STEP 1 & 2

  40. Diagram Modeler Exercises STEP 6: Enter ‘hepatocellular carcinoma’ in the search box and click on ‘Concept’ button. STEP 7: Select the first entry from the list and click on Add Concepts button to add it. STEP 8: Click on OK in the Specify Search Term window to finish adding the new box. continued on next slide… STEP 6 STEP 7 STEP 8

  41. Diagram Modeler Exercises STEP 9: Now we need to add ‘microcalcifications of the breast’ with an AND relationship to the ‘lobular carcinoma’ box, and add ‘fibrosis’ to the ‘hepatocellular carcinoma box’. Using steps learnt before to add a boolean AND relationship, add these search terms Your final diagram should look like this:

  42. Diagram Modeler Exercises Temporal Query Problem: “Get me patients with a benign biopsy followed by a report indicating carcinoma within a year. STEP 1: For a temporal query, we first create the first part of the query just as we did in earlier exercises. Your diagram should look like the one shown here. continued on next slide…

  43. Diagram Modeler Exercises STEP 2: Now we add another query to represent the second part of the query. Right click on any clear area within the box enclosing the query to popup the query menu, and select ‘Add Temporally related sub-query’ from the menu. Your diagram should now look like this: continued on next slide…

  44. Diagram Modeler Exercises STEP 3: Edit the search term box in the second query to specify a ‘carcinoma’ concept. You diagram should now look like this: continued on next slide…

  45. Diagram Modeler Exercises STEP 4:The last thing is specifying the temporal constraint. Double click on the arrow connecting the sub-queries to specify it. Then select the ‘equal/less/greater/ radio button and specify less than 5 years using the widgets. Press OK to finish. continued on next slide…

  46. Diagram Modeler Exercises That’s it. After you press OK, your diagram should look like this: The sub-queries can be as complex as you want and there can be more temporal sub-queries, following the 2nd sub-query.

  47. Dashboard Exercises Dashboard Exercise: Find radial nephrectomy reports that found osteosarcoma but no evidence of renal cell carcinoma. The patients should not be older than 30 years.

  48. Dashboard Exercises Solution:

  49. Diagram Modeler Exercises Diagram Exercise: Find patients who had no evidence of thyrotroph adenoma less than 3 years prior to being diagnosed with Brian Hemangioma

  50. Diagram Modeler Exercises Solution:

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