Importing Lab Normal Values: A Case Study. Henrik Dittmann & Maxime Steisel IT Department, Institut Jules Bordet, Brussels, Belgium

Transcription

1 Importing Lab Normal Values: A Case Study Henrik Dittmann & Maxime Steisel IT Department, Institut Jules Bordet, Brussels, Belgium 1

2 Session Overview Who are we? What do we do with OpenClinica? Why are we concerned about lab normal values? What does our system do with them? What would we like to do in the future? What would you like to do? 2

3 Research IT at IJB Institut Jules Bordet: public and research hospital, specializing in oncology Research IT group: provides IT systems and tools for clinical and translational research investigates new technologies in these areas CTSU (Clinical Trial Support Unit): provides operational support, data management, monitoring, etc. for investigator-initiated clinical trials sponsored by IJB 3

4 OpenClinica at IJB OpenClinica Enterprise Edition, employed largely for investigator-initiated clinical trials since May 2013 Currently 4 active trials, 1 in preparation Typically phase II, subjects, multi-centric, multicountry Rather complex ecrfs: CRFs, study events CRFs built on the base of CDISC CDASH: standardization reusability 4

5 Lab Normal Values It is time consuming to have to enter the lab normal values on every lab CRF. 5

6 Variation in Lab Normal Values LNVs will stay the same across many visits for a subject LNVs will stay the same across many subjects for a site Changes can occur when lab instruments are changed or recalibrated the site switches to another lab the site regularly uses more than one lab + a test is exceptionally done at another lab 6

7 Lab Normal Value References Rather than to enter the LNVs each time, references can be made: to the previous / a specified visit that uses the same LNVs (per subject) to a repository of LNV sheets stored elsewhere in the CRF (per subject) to a repository of LNV sheets independent of subjects (per site, not possible in OpenClinica) Our solution: store LNV sheets in a repeating event allow specification of LNVs in the lab page as well as a reference to an occurrence of the repeating event 7

8 LNV Reference Sheets 8

9 Subject-Independent LNVs Provide users with an external interface for the upload of LNVs: OpenClinica LNV Upload WS enter and update (in case of data entry errors) LNV sheets that will be applicable for all subjects Users can still enter LNVs directly in OpenClinica: in the lab page itself (per lab CRF) as an individual page in the LNV event (per subject) 9

10 User Interface Web interface: authenticate against OpenClinica select site enter CRF data for a new or as an update to an existing LNV sheet Upload of CSV data (planned) Import of HL7 messages (e.g. from LIMS, long-term goal) Scheduled process to add the LNV sheets that have been defined already to any new patients 10

11 Importing an LNV Sheet Implemented as a layer of Web services on top of OpenClinica s SOAP services using a database for recording import data and success as well as study-specific metadata Web Service OC Web Service Internal DB getsites getoccurrences gettests getunits updatelnvs completepatients Study: listall StudySubject: listallbystudy, Event: schedule, Data: import StudySubject: listallbystudy, Event: schedule, Data: import imports tests units oids, imports, values, patients oids, imports, values, patients 11

12 Import process 1) Schedule a new LNV event for each subject in the site; OCC = max(occurrences) 2) While min(occurrences) OCC: Schedule a new LNV event for each subject where occurrence OCC 3) Upload data into the OCC th event for each subject Record OCC, the data itself and success/failure per subject in DB, together with username and timestamp Provide metadata per study in DB: OIDs used, list of tests, list of units 12

13 Examples I Add a new LNV sheet: Update an LNV sheet: PTN-301 L1.0 L1.1 PTN-302 L1.0 L1.1 PTN-303 L1.0 L1.1 PTN-304 L1.0 L1.1 LX1.0 PTN-305 L1.0 L1.1 PTN-306 L1.0 L1.1 PTN-307 L1.0 L1.1 PTN-308 L1.0 L1.1 PTN-309 L1.0 L1.1 PTN-310 L1.0 L1.1 PTN-311 L1.0 L PTN-301 L1.0 L L2.0 PTN-302 L1.0 L L2.0 PTN-303 L1.0 L L2.0 PTN-304 L1.0 L1.1 LX1.0 L2.0 PTN-305 L1.0 L L2.0 PTN-306 L1.0 L L2.0 PTN-307 L1.0 L L2.0 PTN-308 L1.0 L L2.0 PTN-309 L1.0 L L2.0 PTN-310 L1.0 L L2.0 PTN-311 L1.0 L L PTN-301 L1.0 L1.1' --- L2.0 PTN-302 L1.0 L1.1' --- L2.0 PTN-303 L1.0 L1.1' --- L2.0 PTN-304 L1.0 L1.1' LX1.0 L2.0 PTN-305 L1.0 L1.1' --- L2.0 PTN-306 L1.0 L1.1' --- L2.0 PTN-307 L1.0 L1.1' --- L2.0 PTN-308 L1.0 L1.1' --- L2.0 PTN-309 L1.0 L1.1' --- L2.0 PTN-310 L1.0 L1.1' --- L2.0 PTN-311 L1.0 L1.1' --- L2.0 13

14 Examples II Add a new study subject: PTN-301 L1.0 L1.1' --- L2.0 PTN-302 L1.0 L1.1' --- L2.0 PTN-303 L1.0 L1.1' --- L2.0 PTN-304 L1.0 L1.1' LX1.0 L2.0 PTN-305 L1.0 L1.1' --- L2.0 PTN-306 L1.0 L1.1' --- L2.0 PTN-307 L1.0 L1.1' --- L2.0 PTN-308 L1.0 L1.1' --- L2.0 PTN-309 L1.0 L1.1' --- L2.0 PTN-310 L1.0 L1.1' --- L2.0 PTN-311 L1.0 L1.1' --- L2.0 PTN PTN-301 L1.0 L1.1' --- L2.0 PTN-302 L1.0 L1.1' --- L2.0 PTN-303 L1.0 L1.1' --- L2.0 PTN-304 L1.0 L1.1' LX1.0 L2.0 PTN-305 L1.0 L1.1' --- L2.0 PTN-306 L1.0 L1.1' --- L2.0 PTN-307 L1.0 L1.1' --- L2.0 PTN-308 L1.0 L1.1' --- L2.0 PTN-309 L1.0 L1.1' --- L2.0 PTN-310 L1.0 L1.1' --- L2.0 PTN-311 L1.0 L1.1' --- L2.0 PTN-312 L1.0 L1.1' --- L2.0 14

15 Referencing LNVs in Rules Custom Rules Generator: allows data managers to specify rules in an Access database, using generic item names extracts OIDs from metadata exports of testing and production environments creates XML files Syntax extension for rule expressions: $X variable LBREFID eq $X and LBORRES * 2 gt SE_LNV[$X].F_LNV.LBORNHI will be replaced by (using pseudocode here): (LBREFID eq 1 and LBORRES * 2 gt SE_LNV[1].F_LNV.LBORNHI) or (LBREFID eq 2 and LBORRES * 2 gt SE_LNV[2].F_LNV.LBORNHI) or (LBREFID eq 3 and LBORRES * 2 gt SE_LNV[3].F_LNV.LBORNHI) or... 15

16 Working with OC or against it? We don t want to interfere with OpenClinica, modifying or extending the system directly Major architectural change to allow data that is not specific to a study subject Web Services provide an API that (in this case) gives access to all necessary functions Solution does not make use of EE-specific features Working around OC 16

17 Pros and Cons + Support for both site-wide and per-subject LNVs corrections to a LNV sheet propagation to subjects created afterwards o Can be referenced through rules (not efficient, though) Data is really not subject-specific but specific to the site Queries must be addressed for each subject individually Time windows during which manual entry into a subject s LNV sheets can cause the import to fail for this subject 17

18 Outlook 1) Currently, OpenClinica does only cater for study data that is specific to a subject except for some metadata (which is not accessible to rules) ODM provides a place for study-specific reference data in the ReferenceData element 2) Build interfaces to other systems with OpenClinica s web services, e.g., to get LNVs and lab data from LIMS interoperability (read HL7, convert tests, units, ) remove patient information from lab data before importing that 18

19 Thank you for your attention! What would you like to do? dealing with lab normal values dealing with data that are not patient-specific interfacing OpenClinica