HCLS/ClinicalObservationsInteroperability/EMR CT
EMR + Clinical Trials
Abstract
There is great perceived value in being able to work with clinical research data and clinical care data across clinical domains, e.g. health care, pharmaceutical development, pharmcosurveillance. This include the interest to re-use patient data collected in the care context (from EMRs) for data collection points in a clinical research protocol.
Although there is significant overlap in the clinical data content of collected in clinical research and clinical care, the different emerging standard data representations are not taken that into consideration, therefore usage of data across domains is a challenge.
Clinical research data and clinical care data from EMRs have different information models and different terminological standards. CDISC's Study Data Tabulation Model (SDTM), an emerging standard for regulatory reporting of clinical research data, defines the study variables for a given clinical trial in terms of domains and observations. Although many EMRs do not use standards in the modeling of clinical information, there is a large body of work in the Healthcare/Clinical Practice arena where detailed clinical models (DCM) have been developed, e.g. HL7 CDA templates.
The goal of this task is to investigate, and if possible propose, a model that enable re-use of common observation models across the clinical trials and clinical practice contexts. This of course, include how Semantic Web specifications such as RDF/OWL can be leveraged to achieve this.
Task List/Project Plan
- Use Case Scenario with sample Clinical Research Protocols: Rachel
- Demonstration Scenarios:
- 10 Clinical Research Protocols dealing with Labs, Patient Measurements and Diseases/Diagnoses: Rachel
- Functional Requirements Document: Vipul
- Functional Requirements Version 1 with example content and mappings
- Google Spreadsheets Version
- Please e-mail Vipul Kashyap if you need write access to this.
- Mocked Up Patient Data for Diabetes and Hypertension
- Patient Data Set converted to RDF by Eric P
- Creating RDF Representations for Patient Data
- RDF Representation of Patient1 Data based on POMR and Galen Ontologies
- Representation of Patient1 Data based on HL7 RIM and CDA
- RDF Representation of Patient Data based HL7 RIM and CDA
- RDF Representation of Patient1 Data using Detailed Clinical Models
- Updated XML based representation of Patient Data by Tom Oniki
- Initial classification of Entities in Patient 1 by Alan Ruttenberg
- Proposed Patient Care Meta Model by Parsa Mirhaji
- RDF Representation of Patient1 Data based on SDTM
- Brainstorming Slides for the COI Project
- Clinical Data and Information Models based on Data/Functional Requirements
- Collection of Lab Observation Models
- Collection of Medication Models
- Collection of Models for Signs, Symptoms and Diagnoses
- Collection of Models for Physical Examination, e.g., Blood Pressure
- Snippets of HL7 RIM v3.0 represented in RDF/OWL based on the Functional Requirements - Dan Russler
- Detailed Clinical Models
- Clinical Trial Data and Information Models based on Data/Functional Requirements
- Clinical Practice Ontology
- Version 2
- Version 3
- Version 4
- Clinical Trials Ontology
- Version 3
- Computer-based Patient Record Ontoloty
- SPARQL queries
- Using N3 Rules for Clinical Trial Eligibility
- Mappings using N3 Rules
- Mappings from the Clinical Trials Ontology to the Clinical Practice Ontology
- Mappings from the Clinical Practice Ontology to the Database Schema
- Mappings From Clinical Trial Eligibility Drug Information to Prescription in Patient Data Using Drug Ontology
- Rachel's discussion on NDF-RT
- Mary Kennedy's discussion on Snomed and RxNorm
- FDA website on NDC (National Drug Codes)
- Mappings across Clinical Trials and Clinical Practice Ontology
- Mappings from COI patient DB entities to HL7 Vocabulary
- Mappings across vocabularies relevant to the protocol - e.g., Snomed, MedDRA: TBD
- Propose "computable specifications" using OWL 1.1, Rules or both: TBD
- Identify and propose strategies to get access to real world data, esp. healthcare: Jyoti Pathak
- Constructing ontology using HL7 RIM and CDA - Helen Chen
- Project Plan, Goals and Tasks for Proof of Concept
- Current Resource Commitments by various folks
- End To End Demo
- Online COI Demo
- Mock Patient Data for Testing SPARQL statements for CT#8
- Helen Chen presentation on COI Demo
- AMIA 2009 Spring Symposium Presentation
- AMIA 2009 Annual Symposium Presentation
- Mapping from RxNorm to NDC
- SPARQL query transformed to using a healthcare data model (HL7-RIM$DCM
- Final SQL query that hits the database
- Clinical Trial Eligibility Criteria Contradiction Checking Using Rules and Proof
Face to Face November 2007
Tentative Agenda for F2F in November 2007
ISWC HCLS Tutorial 2008
Minutes
Participants
- Stan Huff, Medical Informatician, Intermountain Healthcare
- Aaron Kamauu, RemedyMD
- Jerry Potrado, Roche
- Charlie Barr, Roche
- Amit Sheth, Wright State University
- Joey Coyle, Intermountain Healthcare
- Jyotishman Pathak, Mayo Clinic
- Rachel Richesson, South Florida University
- Bo Andersson, AstraZeneca
- Kerstin Forsberg, AstraZeneca
- Chimezie Ogbuji, Cleveland Clinic
- Yan Heras, Intermountain Healthcare
- Steve Dobson, Pfizer
- Vijay Bulusu, Pfizer
- Susie Stephens, Centocor
- Miguel Valenzuela, Roche
- Tom Oniki, GE Healthcare
- Vipul Kashyap, Partners Healthcare
- Jennifer Fostel, NIEHS, NIH
- Landen Bain, CDISC
- Dan Corwin, Lexikos and SemantxLS
- Joanne Luciano, Predictive Medicine, Inc.
- Eric Neumann, Clinical Semantics Group
- Helen Chen, Agfa Healthcare
- Dan Russler, Oracle
- Matt Moores, Oracle
- Holger Stenzhorn, DERI
Use Case Scenarios
- Rachel Richesson: Use Case Scenario for Screening Patient Populations for Clinical Trial Eligibility
- Use Case Document containing Sample Protocols
- Incorporate Stan Huff's suggestions for use case ... enumerated below:
- Doing mammography
- see nodules or calcifications
- lead to testing ==> breast biopsies
- estrogen receptor results
- lump was benign or malignant
- underlying genetics on BRCA1 gene
- correlate the genetic makeup with phenotypic observations
- ... and so on ...
- Narrow down Choices for Problems/Diagnoses (see Media:HCLS$$ClinicalObservationsInteroperability$UsecaseBackground-EMR-CT-Interop-8-27-07.pdf)
- Initial Functional Requirements Document by Vipul Kashyap
- Susie Stephen: Use Case Scneario based on known drugs in the market
- Need to coordinate with Rachel at some point.
- Jerry Potrado: Propose a narrowly scoped Clinical Trial Design that involves the above examples
- Miguel Valenzuela: Propose a use case scenario based on 21 CFR 11 Regulgations that involves the above examples
- Landen Bain: CDISC High Level Use Case
- Dan Corwin: Core Requirements for a simple matching web service
- Dan Corwin: EMR Wrappers a way to install matching predicates on an EMR system
- Dan Corwin: Search Agents how to automate searches for protocol candidates
- Dan Corwin: : COI Architecture proposed for a prototype use case web app
- Ronan Fox: Use Case Scenario for Clinical Trial Patient Recruitment
Teleconferences
- 7 August 2007
- 14 August 2007
- 28 August 2007
- 11 September 2007
- 11 September 2007 - Kerstin notes
- 18 September 2007
- 25 September 2007
- 2 October 2007
- 9 October 2007
- 9 October 2007 - Bo notes
- 16 October 2007
- 23 October 2007
- 30 October 2007
- 6 November 2007
- 20 November 2007
- 27 November 2007
- 27 November IRC Log
- 18 December 2007
- 8 January 2008
- 15 January 2008
- 22 January 2008
- 22 January 2008 Bo's notes
- 5 February 2008
- 5 February 2008 Holger's notes
- 12 February 2008
- 19 February 2008
- 26 February 2008
- Kerstin and Rachel's Telcon Minutes for 26 February 2008
- Rachel's Telcon Minutes for 4 March 2008
- 11 March 2008
- 25 March 2008
- 1 April 2008
- 8 April 2008
- 15 April 2008
- 22 April 2008
Resources
- The CDISC SDTM ADaM Pilot Project
- HIMSS Project on Integration of Clinical Research with EHR
- Sample Protocols from ClinicalTrials.gov
- Clinical Trials Repository maintained by the NLM
- CDISC Terminologies
- Landen Bain presentation on Patient Profile using RFD
- An evaluation of NCI Common Data Elements
- Clinical Trials Ontology Workshop
- Parallel Universes? Technology in Healthcare and Clinical Development - Paul Bleicher
- Integrating EHR with EDC: When Two Worlds Collide - Paul Bleicher
- Medical Informatics Perspectives on Leveraging the Electronic Medical Record in Pharma
- Lainden Bains CDISC Presentation
- CDISC Terminology Overview
- Future Vision of EHRs as source for Clinical Research
- Chemical Effects of Biological Systems
- Implementation of counted inclusion + exclusion criteria in OWL
- IBM's SHER Usecase: Matching Patient Records to Clinical Trials Using Ontologies
- The Future Vision of Electronic Health Records as an eSource for Clinical Research
- In collaboration with researchers at Columbia University Medical Center) SHER has been used to find electronic patient records that match clinical trials criteria. Pellet, and Fact++ is used in conjunction with Scalable Highly Expressive Reasoner (SHER) as the mechanism for identifying cohorts (amongst 217K+ patients ). SNOMED-CT is used (an expressive Description Logic: EL++) as the ontology for query answering and justification.
- VectorC's CCR$NCI Thesaurus Demo (features include CCR-to-RDF mapping and retrieval of patient subsets using NCI Thesaurus-based reasoning)