Overview of the Comprehensive Research Informatics Suite (CRIS)

Transcription

1 Overview of the Comprehensive Research Informatics Suite (CRIS) CRIS is a robust, multi-application research platform, currently consisting of twenty-five separate open-source software programs capable of functioning together to facilitate research data collection, data submission and study center operations, achieving and maintaining quality data submissions. Through the use of platform integration, any of the platforms can be combined to enhance research data collection and storage for almost any type of medical research. Several additional platforms are currently under development to add to this suite and its capabilities. The members of the CRIS informatics team have years of experience in successfully deploying, and enhancing, open-source informatics solutions for research, as well as developing web-based applications, currently supporting our Cancer Institute and Translational Research Institute. CRIS applications currently in use: 1) Adverse Event Reporting System (AERS): Assesses Adverse Events, AE, based on past issues, adding new AEs as they are identified. Imports lab based AEs from calaegs and stores them within the AE database. Pushes AEs to EPIC and OpenClinica. 2) Adverse Event Reporting System (caaers): Contains the definitions for reports of adverse events which might occur during the data compilation, transfer, extraction or production process. Processes and submits all AERs including electronic AERs, eaer. 3) Lab Adverse Event Grading System (calaegs): Auto-grading Common Terminology Criteria for Adverse Events, CTCAE, V3 and V4 for lab results. 4) Text Information Extraction System (caties): Generates code from free-text path reports. 5) catissue (CT): A management tool for specimen and sample inventory management, tracking, and annotation. Permits users to enter and retrieve data pertaining to collection, storage, quality assurance and distribution of specimens and samples. Currently used by the UAMS Tissue Procurement Facility, in addition to

2 three other departments, which coordinates and oversees the donation, processing, storage and dissemination of tissue specimens and related data. 6) Central Clinical Participant Registry (C3PR): Registers study participants and track consent events. All necessary participant information is entered into this registry. Capable of tracking multiple consent versions, allowing recording of answers to particular yes/no and check-box questions. Also collects familial relationships among the participants as well as household identifiers. Capable of supporting study locations and study phases of both current and new participants across multiple studies. 7) Clinical Research Administrator (CLARA): Used for Institutional Review Board, IRB, protocol and budget management. 8) Event Trackers (ET): Captures and manages study level activities, including status changes, dates, submissions, and services. Contains electronic delegation for each individual study. Supports the creation of pre-study information and data. 9) Family Health Portrait (FHP): Used to collect and store family health history, FHH, and pedigree generation. Allows information to be saved in an XML format. 10) FHH Portal (FHH Portal): Integrates FHP, LS, CT and C3PR for complete pictorial view of data collection status. 11) Harvard Scrubber (HS): De-identifaction tool that is integrated into caties and MC. 12) Label Key (Label Key): Tracks and displays relationship between results from the integrated programs. 13) Life-Ray Portal and Central Authentication Service (LifeRay, CAS): Life-Ray is an open source portal application that hosts all CRIS applications. CAS is a single-signon application which authenticates against the Lightweight Directory Access Protocol, LDAP, in order to eliminate the need for multiple passwords. In the near future, CRIS will be moving to a two-factor authentication system for improved security. 14) LimeSurvey (LS): A robust, user-friendly application for survey data collection which allows the survey administrator to use images in conjunction with surveys and can

3 also identify duplicate and missing data. Enables data-collectors to quickly deliver questionnaires to respondents, collect responses, and analyze or export results in various formats. In addition to a large range of question types and presentation methods, allows for participant management through tokens and branching logic utilizing conditional questions. The Question-by-Question functionality associated with each survey, as well as the Self-Administered Questionnaire, SAQ, and associated evaluation, are all fully functional. 15) MirthConnect (MC): Used for data integration of all CRIS modules, including participant broadcast from C3PR to PSC, CT, caaers, OC, and LS. 16) Open system for Entity Resolution (OystER): An open-source Java application created by faculty, with decades of industry experience in entity resolution, and students at the University of Arkansas at Little Rock, UALR. Because data quality is directly related to data usability, the CRIS team has implemented several open-source tools and processes to ensure usability which we call OystER. We use OystER to identify duplicate references to one entity (participant, participant address, etc.); to find cases where a single reference designates multiple entities; and to process participant data in C3PR. Our experience has been that even small data sets (200 participants or less) are subject to such errors. OystER has detected discrepancies in past studies prior to any given data submission, allowing us the opportunity to make corrections to pre-data submissions. 17) OpenClinica (OC): 21 CFR Part 11 compliant electronic data capture tool that also creates electronic Case Report Forms, ecrfs. Includes discrepancy management and source data verification. 18) Operational Data Elements (ODEs): Data that is derived from a survey such as participant information, consent records, staffing costs, etc. It is the job of the CRIS IMS hub to capture ODEs. 19) Participant Study Calendar (PSC): A Federal Information Security Standards Act, FISMA, and 21 CFR Part 11 compliant application for creating and managing subject activities and study calendars. Provides the ability to create and edit study calendar templates, generate and view calendars of prospective subject activities, track activities as they occur, and manage subject calendars when they change during a

4 study. Accommodates numerous study types, facilitating management of the screening process, registration, active monitoring, and long-term follow-up. Can be used to accurately track the completed activities of a staff member at each visit, as well as capturing event and contact disposition status. Additionally, schedule templates can be created for various types of study visits. 20) Redmine (RM): An open-source, information technology, project management application used to distribute documentation, track issues and manage projects. The CRIS team uses Redmine for project management, issue tracking, bug/defect lifecycle management (reporting, tracking, status, assignment, notes, updates, and resolution), and feature enhancement requests. 21) SQL Server Reporting Services (SSRS): Reports ETL information for file generation. 22) Sugar Customer Relationship Management (Sugar CRM): Customer Relationship Management for community engagement and cancer control. 23) Talend Open Studio (Talend or TOS): Developed by the CRIS team as a data warehouse solution for data analysis, data reporting and data submission to the Data Repository Warehouse, DRW. Thus far, we have created the database schema for the warehouse; developed ETL processes for C3PR and LS databases which also transfers the data into the DRW utilizing Talend; and developed processes to export the data to an XML file that is DRW XML schema compliant. 24) TrialSearch (TrialSearch): Shows basic study information, hosts documents, and, though mainly for use within UAMS environment, does possess limited capabilities for access outside of UAMS. The traininig module is integrated into the ET delegation log. 25) UAMS CORE (Ucore): An online interface that allows researchers to easily access and request varied services offered by different departments and labs across campus. From the Ucore homepage, users select from a list of 19 different subcores ranging from TRI s Clinical Research Services core, to the Genomics Core, to the Tissue Procurement Facility. Each core is set up according to the different services that are provided, but all allow researchers to make service requests and

5 track progress and results from one easy-to-access point. The following database systems are currently in design to be added to the CRIS system in the near future. 1) Foundation 1 (Foundation 1): Database in design. 2) Lexical Enterprise Vocabulary Service (lexevs): Enterprise Vocabulary Service. 3) Open Metadata Repository (openmdr): Metadata repository for data models and CRFs. 4) cabig Array (caarray): Array data storage and management. 5) Genepattern (Genepattern): Pipeline generation. 6) Taverna (Tavern): Webservice and workflow for data analysis. 7) Pre-screening logging system: a management tool for pre-screening workflow.