caTIES User Meeting 2011

1. caTIES User Meeting 2011 Introducing caTIES 4.0 Associate Professor, Department of Biomedical Informatics, University of Pittsburgh, School of Medicine crowleyrs@upmc.edu Rebecca Crowley

2. Welcome • Welcome to all our users and partners! • In person and webinar introductions • Many types of users here with us today • Planning yearly User Meeting through the next five years

3. Purpose of this meeting • Build user community • Find out how you are using caTIES • Get your feedback on the current product • Learn more about barriers to adoption • Provide most up-to-date information. Sow seeds for future opportunities (nationwide virtual tissue-bank, etc.) • Gather your ideas and requirements for future releases

4. Sessions for Today 9:00 - 9:55 AM - Session 1 Welcome – Michael Becich, University of Pittsburgh Department of Biomedical Informatics Chair Introducing caTIES 4.0 – Rebecca Crowley, caTIES Principal Investigator 10:00 - 10:55 AM - Session 2 caTIES 4.0 Demo – Girish Chavan, caTIES Project Manager caTIES 4.0 Sectioning, Tagging & Configuration Tool – Girish Chavan 11:00 - 12:30 PM - Session 3 Resources for End User Support – Rebecca Crowley TIES End User PanelMichaele Armstrong - Regulatory Specialist, Endocrine Surgery, UPMC Michelle Bisceglia - Manager, Health Sciences Tissue Bank, Pitt/UPMC Yang Liu - Assistant Professor, Medicine/Division of Gastroenterology, Hepatology and Nutrition and Department of Bioengineering, Pitt/UPMC -- 60 min. Lunch Break –

5. Sessions for Today 1:30 - 2:55 PM - Session 4 caTIES Institutional Users, Progress Reports & Emerging Needs David Carrell – Group Health Cooperative, Seattle, Washington Tara McSherry – University of Pennsylvania, Philadelphia, Pennsylvania UmitTopaloglu – University of Arkansas, Little Rock, Arkansas 3:00 - 3:55 PM - Session 5 caTIES Future Directions – Rebecca Crowley 4:00 - 4:55 PM - Session 6 caTIES Open User Forum – Hosted by Rebecca Crowley

6. The past year… • Held first caTIES Annual User Meeting in January 2010 Participants: 4 onsite and 25 webinar participants • 2 major releases; v3.6 and v3.7 • Held 6 caTIES Office Hour sessions from March to August 2010 Some community statistics since January 2010 • 878 downloads • 200+ forum posts • 3,000 unique visitors to caTIES website. 2,000 pageviews/month on Sourceforge. 25 requests for caTIES demo accounts • 80+ local users A strong, active and growing community of users!!

7. History - 1 • Chapter 1 - Shared Pathology Informatics Network • NCI Sponsored U01 (Collaborative Consortium) • Harvard, UCLA, Regenstreif, Pittsburgh • NLP tools, ideas, first demonstration of data-sharing • Chapter 2 - caBIG • Large multi-CC contract/community developing architecture + open source, interoperable systems for cancer research community • caTIES code base • Security Architecture • Grid Communications • User Interface • Version 1 and 2 • Four institutions sharing some data, IRB protocol Penn-Pitt

8. History - 2 • Chapter 3 – University of Pittsburgh CTSA Project • Deployed at University of Pittsburgh • Worked with Tissue Bank • Set up honest brokers • Policies and Processes • IRB issues • caTIES v3 • Chapter 4 - caTIES NCI funded project • More autonomy • Stable, consistent release cycle • User community • New features • Does not include the stuff you all are doing – that we don’t even know about!!!!

9. Details of our new NCI grant • Continued Development of Software R01 • New platforms and DBMS, new features, new report types and formats and auditing • Evaluation • Development of User Community and Support • Yearly user meetings • Forums and other communication TBD • Pilot projects in Y4 and Y5

10. Features added in 2010 • Support for Linux and Oracle • Section based searching • Text searching within orders/case sets • UI revamp based on usability studies • Labeling for case sets • Email Support – Emails for account creation/updates, order submission and order status changes • Support for strong passwords • Activity logging – All queries can be logged • caTIES Status Dashboard • Numerous bug fixes and improvements to the installer

11. Introducing caTIES 4.0 New Features • Tagging • Configuration Tool • Improvements to Status Dashboard • A fresh look for the UI

12. What’s planned for 2011? • Two more releases in June and December • Have a working caTIESNet with at least two nodes • Strong focus on caTIESNet security, features and enhancements • Continue focus on improving installation and configuration experience • Radiology reports • Schedule caTIES Office Hours for two months after every release Session Five (3:00pm – 3:55pm) will cover future directions in more detail.

13. Questions?

14. caTIES 4.0 New Features Sectioning | Tagging | Configuration Tool Product Manager, Department of Biomedical Informatics, University of Pittsburgh Girish Chavan

15. caTIES 4.0 DEMO

16. Sectioning

17. Section Configuration • Configuration options combined from four different configuration files to one table in the database. • Section_Type table lets you choose which sections to de-identify, concept code, index and display on the client. Exact copies of the table are maintained in both public and private databases by the DeidPipeController. • Specify if you want to use, whitespace, keyword or standard analyzer for indexing. • Mechanism can be used to add searchable metadata for each report, making it extremely adaptable and extensible to individual needs. e.g. Tagging

18. Section_Type Table NAME: A pretty name for this section. LIMS_CODE: An external system name for this section. e.g. HL7 feeds typically denote Final Diagnosis sections as ‘FIN’ IS_HISTOGRAMMED:Section has a value domain for its contents. This is used so that the client can generate a picker when searching this section type. PRIORITY: Specifies the relative position of this section within the report text. IS_VISIBLE:If this section is displayed in the client. IS_KEYWORD: Use a Keyword Analyzer when indexing this section. • IS_PUBLIC_TAG: A misnomer. Use a Whitespace Analyzer when indexing this section.

19. Default Section_Type Table

20. Pipelines and Sectioning • Initializes the section_type table from sectionheaderconfig.txt on private and public databases • Builds report text from the sections and creates a path_report row in public database. • Indexes the sections for which INDEXED flag is set. Lucene Analyzer is selected based on the IS_KEYWORD or IS_PUBLIC flags. • Extracts the sections from the document text and creates report_section rows.

21. Section Processing Flowchart Start Is section_type table empty? DeidPipeController bootstraps the section_type table from SectionHeaderConfig.txt YES NO DeidPipeController assigns section types to sections and builds the report text from the sections. IS_DEIDENTIFIABLE sections are additionally de-identified. IS_CODEABLEsections are coded by TiesPipeController IS_INDEXABLE sections are indexed by IndexPipeController Client gets section list from clientconfig.xml Finish

22. Section Searching • Each indexable section type is a separate field in the index. Field name is document_text_<section type name> • Sections are analyzed but not stored in the index. • caTIES client reads the searchable sections from the <tomcat>\webapps\caties\conf\clientconfig.xml file. • Next caTIES release will have the client initializing from the section_type table.

23. Tagging

24. When to use tagging? To limit searches to: • patients/reports in a specific clinical trial • patients/reports identified matching a certain criteria from another system • reports belonging to a specific hospital • essentially any user defined partition of the dataset. e.g. reports with scanned images

25. How does it work? • Uses the sectioning mechanism. • Tags are either system level or protocol level. • Defines a section type with name ‘REPORT_TAG’. IS_HISTOGRAMMED, IS_PUBLIC_TAG and IS_INDEXABLE is true and IS_VISIBLE is false. • Client looks for histogram values for REPORT_TAG section type from the Section_Value_Histogram table in the public database. • In future releases, tagging will have a two-level hierarchy, i.e. tag type and tag value. This will let users organize the tags in a meaningful way.

26. System Level Tagging Visible to all researchers in the system Steps: • Create separate HL7 document directories for each tag • Configure the HL7PipeController • Set the hl7.directory parameter • Set the ‘caties.hl7importer.tag’ parameter • Tag names cannot contain spaces • Run the HL7PipeController for each directory, changing the tag parameter between runs.

27. Protocol Level Tagging Visible only to users registered in a specific protocol. Only Honest brokers on the protocol can create the tags. Steps: Create a list of MRN/SSN numbers in a comma separated value(csv) file. Login as honest broker on the protocol and launch the Tagging Dialog. Enter the tag name, and select the csv file that contains the patient identifiers. Click ‘Start Tagging’. Wait up to 24 hours for the tagged records to be processed by the IndexPipeController and make it into the search index.

28. Configuration tool

29. Configuration Tool • Single tool to configure all caTIES components. • Installed in <catiesinstallationdir>/configuration directory. • ‘run_configuration_tool.bat (.sh) will launch the configuration tool. • Detects which services are installed, and reads current configuration values from files. • What’s next? • Triggering processing of reports through pipelines (Setting the application_status field) • Adding/removing/configuring sections for coding/deidentifying etc. • Adding/removing tags. • Eventually, everything related to customizing a caTIES installation

30. caTIES User Meeting 2011 End User Support Resources Associate Professor, Department of Biomedical Informatics, University of Pittsburgh, School of Medicine crowleyrs@upmc.edu Rebecca Crowley

31. TIES – Our caTIES Implementation • Launched in early 2009 with new branding and customization to support structured ordering instructions. • Marketing effort launched late 2009. Monthly TIES luncheons to introduce users to the system. • Advertisements in university publications and mailing lists. • Increased user base from 18 users to 100+ users. • User support includes helpdesk support, training classes, online videos and user manual.

32. TIES Website http://ties.upmc.com Account Request Forms Training Videos User Manual

33. Flyer

34. Additional Resources • Sample advertisements for TIES in Pitt & UPMC communications. • Sample Implementation Plan • Details various tasks and phases of an institution wide caTIES implementation. • UPMC TIES Usage Policies • Very detailed policies governing account creation, individual responsibilities and turnaround times.

35. caTIES User Meeting 2011 Future Directions Associate Professor, Department of Biomedical Informatics, University of Pittsburgh, School of Medicine crowleyrs@upmc.edu Rebecca Crowley

36. Future Versions • Funding and effort to continue with two versions per year over the next three years. • Version 4.1 scheduled for June, 2011 • Version 4.2 scheduled for December, 2011 • As always, we want to give your emerging needs priority in our development plans

37. Future Version • Version 4.1 - June, 2011 • Core distributed systems enhancements Phase I • Administrator and Orders UI overhaul to support larger number of users • Tagging system enhancements • Configuration tool enhancements • caTIES status dashboard enhancements

38. Future Versions • Version 4.2 - December, 2011 • Core distributed systems enhancements Phase II • Authentication Enhancements • Support for local LDAP/Active Directory • Billing component or interface? Delivery components or interface?

39. R01 research Plans • Evaluation of recall of the system compared to Cancer Registry • Radiology reports and evaluation

40. Future Issues • Need to re-evaluate the coding pipeline • Benefits and drawbacks of continuing to use MMTx • Potential for using IndexFinder or for changing to cTAKES • Vocabularies • Relationship to ODIE

41. Future Issues • Need to re-evaluate security infrastructure • Many new developments in this area • De-identification a continued problem • iDASH (new University of California San Diego NCBC focused on data sharing) • CTSA developments

42. Future Issues • Need to re-evaluate caBIG relationship • Should we expend effort to maintain compliance, especially since that’s changing • Relationship to caTISSUE

43. Towards a collaborative network • Development of collaborative network nearing feasibility • Funding – initial seed funding possibly through CTSA SPIRiT consortium or linked R01 • Benefits to all other possible contributors • Participation by other centers

44. caTIES User Meeting 2011 Open Forum Associate Professor, Department of Biomedical Informatics, University of Pittsburgh, School of Medicine crowleyrs@upmc.edu Rebecca Crowley

45. Institutional Users and End Users • How are we doing? • What emerging needs are we missing? • What are your end-users saying? • What improvements can we make in our processes? • Releases • Documentation • Notification • Support

46. Where should this project go? • Where do you want to see this project go? • Interest in collaboration on grants submitted this year? • What is the level of interest of institutions in the Collaborative Network? • Perceptions at NIH • What can we learn from past efforts • Approaches (including bottom-up end-user collaborations)

47. Where should this project go? • What are the unrecognized benefits of this system as a platform for other development efforts? • Other documents? • Images? • Targeted Information Extraction • Interoperability with other systems • Community development? • What are the benefits and drawbacks of pursuing relationship to other EMR related warehouse, sharing and analysis efforts (i2B2, iDASH etc)?