Department of Biomedical Informatics University of Pittsburgh School of Medicine Elizabeth Legowski

Introduction to TIES TIES stands for Text Information Extraction System Deployed UPMC-approved system for retrieving data and identifying and ordering tissue Currently contains 4 million de-identified surgical pathology reports from 2003-present across all UPMC hospitals –Updated monthly and automatically from clinical systems

Introduction to TIES De-identification Access from anywhere Concept-based queries Hierarchical indexing Negation Temporal queries Honest broker support Role-based access

Introduction to TIES

Introduction to TIES Search for reports –Facilitate researchers Filling tissue orders –Assigned as honest broker to protocol –Set item status, order status

Introduction to TIES Access the TIES Application Submit account requests How to videos and manuals Get status updates Helpdesk contact information

Logging In Windows / MAC / Linux Java 1.5+ –Download latest version at

Logging In The TIES client is served as a Java Webstart application To access TIES: 1.Access the website: 2.Click the ‘Launch TIES’ button: 3.Click the ‘Run’ button on the Java Webstart window. It will take a short time to download the TIES application to your computer. Fortunately, this only happens the first time you are accessing TIES. After Webstart has finished downloading, you will be asked to pick a data network to access.

Logging In 1.Select ‘Test Data Network’ from the drop down box and then click the ‘OK’ button The Test Data Network contains dummy data (not real data) and is used for training purposes.

Logging In 2.Enter your username and password and click the ‘Login’ button. Logging in takes about 1 minute.

Logging In For TIES users, there are three roles to choose from: Honest Broker, Researcher and Preliminary User. 3.Select ‘Preliminary User’ as the role from the drop down box, and the appropriate study. Click on ‘OK’ to finish the logging in process.

Logging In 4.Read USAGE AGREEMENT and click ‘Accept’ if you agree to the 3 terms provided in the box.

Preliminary User Perspective Current role and distribution protocol for this session Tool bar provides quick access Tab bar is used to switch between open tabs

Preliminary User Perspective Query Builder pane Dashboard View Select report type and sections to search Switch query views ‘Start Search’ and ‘Start Over’ buttons Type search terms here Chart options Switch between query and results ‘Advanced Dashboard’ link

Preliminary User Perspective Query Builder pane Text search not available in ‘Preliminary User’ perspective At least 1 of the search terms must be present Advanced Dashboard Search term must be present in the negated form All of the search terms must be present ‘Start Search’ and ‘Start Over’ buttons

Preliminary User Perspective Diagram View Currently selected filter Query Builder Pane Filters palette for adding and deleting filters. Filters can also be added by right clicking in the diagram. ‘Start Search’ and ‘Start Over’ buttons

Dashboard Query Builder The simple dashboard query works very much like a Google™ search bar. It is designed for very basic queries like: “Search for reports with adenocarcinoma” TIES selects the best matching NCI metathesaurus concept for each search term entered, and returns the reports that contain the concept. If there are multiple search terms, the returned reports contain all of the matching concepts. Enter search terms here NOTE: Race is NOT consistently captured on UPMC System

Dashboard Query Builder If a word is misspelled, it will appear with red wavy lines underneath, like this: To correct the spelling, right click on the word and choose the correctly spelled word from the drop downs. Preliminary Users are not able to create Temporal Queries at this time. Print Screen function can capture results which can be placed in grants, reports and preliminary research documents. All Dashboard queries (Basic or Advanced) will translate into Diagrams when you switch to the Diagram View. However, not all Diagram queries can be shown in the Dashboard View.

Dashboard Query Builder Treating search terms as Concepts generally returns more accurate results. Concept searching returns reports containing the search term, as well as reports containing 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 also return reports containing BOOP, COP, and any other synonyms of BOOP. In the Advanced Dashboard, search terms entered in the NOT box (bottom empty search box) should be absent from the report text when doing a Text search. When performing a Concept search, the search term will need to be presented in the negated form within the report. –For example, if you enter ‘Adenocarcinoma’ in the NOT box for a Text search, it will return all reports that do not contain the word ‘Adenocarcinoma’. If you do a Concept search, only reports containing phrases such as ‘No evidence of adenocarcinoma’ or ‘Adenocarcinoma not found’ will be returned.

Dashboard Query Builder Queries with a single word search term Problem: Search for pathology reports with adenocarcinoma. STEP 1: Type ‘adenocarcinoma’ in the search box. The text will turn blue once it matches to a concept. STEP 2: Select the ‘Pathology’ checkbox under Report Types to limit your search to pathology reports. STEP 3: Click on ‘Start Search’ button. STEP 3 STEP 2 STEP 1

Browsing Results Can change sub- & category Can change type of chart displayed Matches categorized by ‘Event Year’ 10 Matches from Matches from 2011 Bar Chart View Chart Legend Number of matches returned in ‘any section’ Hit ‘Update Chart’ button if any changes are made to chart type or categories

Dashboard Query Builder Changes to query results Problem: Change chart type to a pie chart showing age distribution. STEP 1: Click on ‘Pie’ Chart Type. STEP 2: Click on ‘Age’ in Categorize By drop down menu. STEP 3: Click on ‘Update Chart’ button. STEP 1 STEP 2 STEP 3

Browsing Results Highest number of matches in age range Color coding for age range legend Pie Chart View Each age range shown

Dashboard Query Builder Queries with a multi-word search term Problem: Search for reports with atypical ductal hyperplasia. STEP 1: Since “atypical ductal hyperplasia” is one concept, we type these words in the ‘All of these Concepts’ field. Type ‘atypical ductal hyperplasia’ in the search box. STEP 2: Click on ‘Start Search’ button. STEP 2 STEP 1

Dashboard Query Builder Queries with multiple concepts Problem: Search for reports with biopsies indicating atypical ductal hyperplasia. STEP 1: Type ‘atypical ductal hyperplasia’ in the search box, a comma ‘,’, and then type ‘biopsy’. STEP 2: Click on ‘Start Search’ button. STEP 2 STEP 1

Dashboard Query Builder Queries with demographics Problem: Create a bar chart of year old females with atypical ductal hyperplasia categorized by event year. STEP 1: Type ‘atypical ductal hyperplasia’ in the search box. STEP 2: Under Report Types, select the Pathology checkbox. STEP 3: Under Age, select ‘ranging between’; type ‘30’ in the Min box; type ‘40’ in the Max box. STEP 4: Select ‘Female Gender’. STEP 5: Choose ‘Bar Chart’. STEP 6: Categorize by ‘Event Year’. STEP 7: Click on ‘Start Search’ button. STEP 5 STEP 4 STEP 1 STEP 3 STEP 6 STEP 2 STEP 3

Researcher Perspective Click on ‘Switch Role’ button and change to ‘Researcher’ perspective

Researcher Perspective Read USAGE AGREEMENT and click ‘Accept’ if you agree to the 4 terms provided in the box.

Researcher Perspective Can now set “Number of Results” Note expanded toolbar

Advanced Dashboard Query Builder For more advanced queries, switch to the “Advanced Dashboard” by clicking on the blue link under “More options?” To switch to the ‘Advanced Dashboard’ – click on this blue link

Advanced Dashboard Query Builder To switch back to the ‘Basic Dashboard’ - click on this blue link 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. Same as ‘Basic Dashboard’ box Additional search boxes let you specify boolean OR and NOT logic Specify demographic criteria for patient here Select ‘Concept’ to map the search terms to NCI metathesaurus concepts and search with those concepts. Select ‘text’ to treat the search terms as text strings.

Advanced Dashboard Query Builder Queries with OR Problem: Search for reports with nevus or melanoma. STEP 1: Type ‘nevus’ in the OR search box, followed by a comma ‘,’ and ‘melanoma’. STEP 2: Specify the ‘No. of Results:’ to ‘100’. STEP 3: Click on ‘Start Search’ button. STEP 1 STEP 3 STEP 2

Browsing Results Report results in text format Report details Choose how report text is visually displayed Patient details Results in tree format. Reports grouped by patient. Click on any report in the tree to view. Can save reports in separate case sets. Later, case sets can be viewed or submitted as orders for tissue. ‘Change’ returns to original query

QA Options Two QA options are available in the File menu: –Request Review  Use for flagging problematic reports (ex: report doesn’t fit search criteria, concepts are not colored correctly in the annotations) –Quarantine  Use for reports that are not completely de- identified.  Once quarantined, reports are not available for searches until un-quarantined by a system administrator.

Diagram Query Builder Diagram button Initial diagram with a single search term box Filters palette for adding and deleting filters. Filters can also be added by right clicking in the diagram.

Diagram Query Builder 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 placeholders, ‘All Reports’ and ‘Filtered Reports’, are special boxes that represent the start and end of the diagram. The results of the query are all the reports that make it to the ‘Filtered Reports’ Placeholder. Forks in the path indicate boolean OR conditions. Filters on the same path are logically ANDed together.

Diagram Query Builder Report Type Search Term NOT Search Term Event Year Gender Age

Diagram Query Builder Right clicking on any part of the diagram will display a context sensitive menu –Add/remove filter boxes, edit filter properties, or add/remove temporal sub-queries –Menu options 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 filter box by dragging any of the 8 small squares displayed around it when selected. Filter boxes (except the ‘All Reports’ and ‘Filtered Reports’ placeholders) can be deleted by: –Selecting it and pressing the ‘Delete’ key on the keyboard OR –Right clicking on the filter box and selecting ‘Delete Filter’ Can also use the Filters palette to add/remove filter boxes

Diagram Query Builder Query requiring Boolean AND Problem: Search for reports with biopsies indicating atypical ductal hyperplasia. STEP 1: Right-click on the green ‘Search Term’ box. A dropdown menu will appear. Choose Edit filter properties. Alternatively, double click the green ‘Search Term’ box. STEP 2: Type ‘atypical ductal hyperplasia’ in the ‘add concept here’ textbox STEP 3: Click the + button, or press Enter. STEP 4: Select the term(s) that best fit(s) your concept. 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 the ‘Done’ button. continued on next slide… STEP 1 STEP 2 STEP 3 STEP 4 STEP 5

Diagram Query Builder STEP 6: Step 5 will send you automatically back to the original ‘Search Term Filter Properties’ popup window. Click the ‘Save’ button. To add a filter box for biopsy we will use the Filters palette on the left-hand side of the screen: STEP 7: Click the button in the Filters palette. STEP 8: 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 6

Diagram Query Builder Query with Boolean OR Problem: Search for reports with either lobular carcinoma with microcalcification in the breast or primary carcinoma of the liver with cirrhosis. STEP 1: We will reuse the empty search term box that is added when a new query is created. Modify its properties to add ‘breast’ as a concept. STEP 2: To add ‘liver’, with an OR relationship to ‘breast’ we will select the ‘breast’ box as the reference box and right click. From the dropdown menu, choose ‘Add ORed Filter’ and click ‘OK’ for ‘Search Term’ filter type. STEP 3: Type ‘liver’ in the ‘add concept here’ textbox. STEP 4: Click the + button, or press Enter. STEP 5: Select the term(s) that best fit(s) your concept. STEP 6: Click the Select Concepts ‘Done’ button. STEP 7: Click the ‘Save’ button. continued on next slide… STEP 1 STEP 2 STEP 3 STEP 4 STEP 6 STEP 7 STEP 5

Diagram Query Builder STEP 8: Now we need to add ‘lobular carcinoma' and ‘microcalcification’ with a boolean AND relationship to the breast box, and add ‘primary carcinoma' and ‘cirrhosis’ to the liver box. Using steps learned before, add these search terms. Your final diagram should look like this:

Diagram Query Builder Temporal Query Problem: Search for patients with a benign biopsy followed by a report indicating carcinoma within 5 years. STEP 1: For a temporal query, we 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…

Diagram Query Builder 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. Alternatively, click the Patient Event button in the Filters palette. Your diagram should now look like this: continued on next slide…

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

Diagram Query Builder STEP 4: The last thing is specifying the temporal constraint. Double click on the arrow connecting the sub- queries to specify it, or right click the arrow and select ‘Modify Temporal filter properties’. 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…

Diagram Query Builder Now, your diagram should look like this: The Patient Events can be as complex as you want and there can be more temporal events following Patient Event 2.

Diagram Query Builder Diagram Exercise: Find patients who had no evidence of thyrotroph adenoma less than 3 years prior to being diagnosed with Brain Hemangioma

Diagram Query Builder Solution:

Saving & Loading Queries You can save queries in TIES for later retrieval by using the ‘Save Query’ button or ‘Save Query’ and ‘Save Query As’ options in the file menu. The ‘Save Query As’ dialog box is shown here: Queries already saved by this user Name and description for the query

Saving & Loading Queries You can open queries previously saved by you, or other members of your distribution protocol. Go to File and choose ‘Open Query’. The ‘Open Query’ dialog box is shown here: View queries created by others using the dropdown menu here

Honest Broker Perspective Can search using identifiers Note expanded toolbar

Honest Broker Perspective Name, MRN, and SSN shown in Patient Details Accession number shown in Report Details.

Tissue Orders Researchers can group reports into case sets. Case sets can be used to group interesting cases together and can be viewed and modified by all researchers in the distribution protocol. Case sets can be submitted as orders for tissue/data. Tissue ordering in TIES is a multi-step process involving communication with the honest broker to confirm the order.

Tissue Orders Step 1: Create a case set Researcher Path reports, additional info My Case Sets Tab

Tissue Orders Step 2: Submit the order Researcher SubmitAdd to queue Honest Broker

Tissue Orders Step 3: Verify the order Honest Broker 1.Examine IRB approval 2.Verify tissue availability 3.Update status of each order item. Status options are Not Found, Retrieved, Unusable, Reviewed, Processed, Distributed

Tissue Orders Order Item status can be any of the following. It can be set only by the Honest Broker. Not Found – The requested tissue for this order item was not found in the tissue bank. Unusable – The tissue was found, but was not usable. For example, too little tissue was left on the block. Retrieved – The requested tissue was retrieved successfully from the Tissue Bank and is usable. Reviewed – The tissue has been reviewed by the Tissue Utilization Committee and approved for distribution. Processed – The tissue has been prepared for distribution. Distributed – The tissue was picked up/shipped to the researcher.

Tissue Orders Step 4: Request confirmation from the researcher Researcher Set order status to retrieved or incomplete Add to awaiting confirmation queue Honest Broker

Tissue Orders Step 5: Confirm the order Researcher Confirm order Add to confirmed queue Honest Broker

Tissue Orders Step 6: Fulfill the order Honest Broker 1.Cut tissue/slides 2.Ship tissue to PI/hold tissue for collection by PI 3.Update order status to Distributed

Tissue Orders Order status can be any of the following. They are displayed in the general order of occurrence Pending – The order has been submitted by the researcher and is in the honest broker’s queue. Reviewing – The order is being reviewed by the Honest Broker. When an order status is switched to this, it is displayed in the ‘In Process’ group in the Manage Orders Tab. Incomplete – Not all the requested tissue was available/usable. Awaiting confirmation from researcher for further processing of order. When an order status is switched to this, it is displayed in the ‘Awaiting Confirmation’ group in the Manage Orders Tab. Retrieved – All the tissue requested was successfully retrieved from the tissue bank. Awaiting confirmation from researcher for further processing of order. When an order status is switched to this, it is displayed in the ‘Awaiting Confirmation’ group in the Manage Orders Tab. Confirmed – The researcher confirms the order to be processed. Processed – The tissue/slides have been prepared for distribution. When an order is in the following states, it is displayed in the “Completed Orders” group in the Manage Orders tab. Distributed – The tissue was picked up/shipped to the researcher. Cancelled – The order was cancelled by the researcher.

Tissue Orders Researchers create case sets by clicking the + button under Case Sets in the Results view. Reports can be added to existing case sets by dragging reports to the desired case set, or using the Add To button and choosing the appropriate case set.

Tissue Orders Submit or delete an order here Case set name All orders are classified into Case Sets, Submitted, or Completed orders 6 reports added as order items. Click on an order item to load its view in the right pane. Order View

Tissue Orders Area to specify ordering instructions specific to this case De-identified pathology report for this case

Tissue Orders Researchers can submit a case set by selecting it in the ‘My Case Sets’ tab and clicking on the ‘Submit’ button in the ‘Available Tasks’ section. TIES will add the order to the honest broker’s queue. It will also move the order to the ‘Submitted Orders’ group for the researcher.

Tissue Orders Honest brokers have access to identified data for reports when viewing them as part of a search result or a submitted order. Honest brokers have a ‘Manage Orders’ tab that displays all orders that have been submitted to them. They can modify these orders, and update status for the orders and individual order items here.

Tissue Orders A new order with 2 order items. Clicking on any order item opens its detailed view in the right pane. Order information includes name and address of order creator and IRB information Orders are classified into these categories.

Tissue Orders Ordering instructions are specified by the researcher before the order is submitted. Select the status of the order item and click ‘Save’ to change the status. Information for each order item includes, the identified report information such as Accession no., and identified patient information such as name, SSN, MRN etc.

Tissue Orders Honest Brokers can add order items to pending orders that are present in their queue. Searching as an Honest Broker is similar to the Researcher’s search perspective. Honest Brokers can search with identifiers, and are shown additional identified information in addition to the de-identified information when viewing a report in the search results.

Rebecca Crowley Jacobson (Principal Investigator) Girish Chavan (Product Manager) Kevin Mitchell (Senior Developer) Eugene Tseytlin (Senior Developer) Elizabeth Legowski (User Support)