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Strategic Health IT Advanced Research Projects (SHARP) Research Focus Area 4 - Secondary Use of EHR Data Increasing efficiency of patient care through electronic healthcare records
Mayo Clinic, long a leader in the science of health care delivery, is proud to be a recipient of the Strategic Health IT Advanced Research Project award. The SHARP Program – part of the Office of the National Coordinator for Health Information Technology, is focused on improving quality, safety and efficiency of health care through Information Technology.
Area four's SHARP project will enhance patient safety and improve patient medical outcomes through the use of an electronic health record. Traditionally, a patient’s medical information, such as medical history, exam data, hospital visits and physician notes, are stored inconsistently and in multiple locations, both electronically and non-electronically. We propose research that will generate a framework of open-source services that can be dynamically configured to transform EHR data into standards-conforming, comparable information suitable for large-scale analysis, inferencing, and integration of disparate health data.
Area four's mission is to enable the use of EHR data for secondary purposes, such as clinical research and public health. By creating tangible, scalable, and open-source tools, services and software for large-scale health record data sharing, this project will ultimately help improve the quality and efficiency of patient care through the use of an electronic health care record.
Announcements
- All SHARPn current and past announcements can be found here.
SHARPn work Showcased at AMIA 2013 Annual Symposium
- November 16-20, 2013
- Washington DC, Washington Hilton
On Monday, November 18, 2013, 8:30 AM - 10:00 AM; International Ballroom East (Washington Hilton) Featured Presentation (S11) - The SHARP Program and the Next Generation of Health Information Technology
- SHARPn Presentations
SHARPn PhenotypePortal 1.0 Release
- November 17, 2013
The Strategic Health IT Research Project for Secondary Use of Electronic Health Record data (http://sharpn.org) is pleased to announce the public release of PhenotypePortal (http://phenotypeportal.org). This effort represents a culmination of work by SHARPn members from the High-Throughput Phenotyping (HTP) team at Mayo Clinic, Intermountain Healthcare, and Agilex Inc. to provide a robust infrastructure for standards-based representation and execution of cohort identification algorithms.
Key features of PhenotypePortal
- Applies Meaningful Use (MU) terminologies and Quality Data Model (Version 2.0) for representation and authoring of cohort definition and phenotyping algorithms
- Uses open-source Common Terminology Services (CTS2) for terminology and value set management
- Uses open-source JBoss Drools business logic integration platform for automated execution of cohort algorithms
- Execution results for MU Stage 2 Eligible Provider and Eligible Hospital Clinical Quality Measures (CQMs) validated against Project Cypress
- Leverages Clinical Element Models and cTAKES natural language processing engine for standardized and normalized clinical data representation
Release details
- Documentation and installation instructions: http://docs.phenotypeportal.org
- API demonstration: http://api.phenotypeportal.org
- Virtual Machine image: http://static.phenotypeportal.org/downloads/vm/sharp-htp.ova
- Cypress execution report for MU Stage 2 CQMs: http://api.phenotypeportal.org/executor/cypress/report
- Source code: https://github.com/SHARP-HTP/qdm-phenotyping
Dr. Doug Fridsma and Avinash Shanbhag visit with members of the SHARPn team at Mayo Clinic
- August 15, 2013
Dr. Doug Fridsma, Director of S & I and SHARP Program and Avinash Shanbhag, SHARP Program Officer visit with members of the SHARPn team.
- Data Normalization - Dr. Hongfang Liu
- UIMA - Marshall Schor
- Natural Language Processing (NLP) - James Masanz / Dr. Hongfang Liu / Dr. Guergana Savova
- Data Quality - Dr. Susan Rea / Dr. Kent Bailey
- High-Throughput Phenotyping (HTP) - Dr. Jyoti Pathak
cTAKES is a top level Apache Software Foundation project!
- March 20, 2013
Apache Software Foundation voted positively to move cTAKES from an incubator stage graduating cTAKES to a top-level Apache project. In the last 9 months, we have built an international multi-institutional community of contributors, committers, and followers. This is a great achievement!
Its URL will soon change from http://incubator.apache.org/ctakes/ to http://ctakes.apache.org
2013 SHARPn Work Showcased at HIMSS 2013
- March 4-7, 2013
Live demonstrations of a secondary use of electronic health record data to electronically identify patients’ physical characteristics (phenotypes), allowing for research into population health and clinical workflow.
2012 SHARPn Summit "Secondary Use"
- June 11-12, 2012
Building solutions that matter
- Enabling secondary use of EHR data to generate new
- knowledge, improve care, and address population needs
SHARPn—one of the grantees of the Strategic Health IT Advanced Research Projects (SHARP) program—would like to invite you to its 3rd annual meeting on June 11-12, 2012 on the University of Minnesota Rochester Center campus to present and discuss work in the following areas:
- Standards, Data Integration & Semantic Interoperability
- Natural Language Processing
- Phenotyping: clinical trial selection, clinical decision support, quality measurement
- Software evaluation
Attendees will:
- Learn more about SHARPn and the health IT field
- Explore technologies and tools that enable secondary uses of EHR data
- Participate in a hands-on tutorial from experts on how to better leverage secondary data using open source tools
- Present your paper or poster on related topics through a peer reviewed process
- Work side-by-side with community leaders to develop and refine customer and stakeholder requirements
Join Us Remotely:
- US Toll-free: 1-866-365-4406
- Switzerland Toll-free: 0-800-700-286
- Access Code: 293-3780#
- Participant phone lines will be muted; you may type questions in the web chat room.
- Meeting URL https://www.callinfo.com/prt?host=globalcrossing&an=8663654406&ac=2933780
- Summit Webcast Schedule
Agenda & Presentations
- Summit Agenda Flyer
- SHARPn Summit Program
- Monday, June 11, 2012 - Presentations & Meeting Notes
- Tuesday, June 12, 2012 - Presentations & Meeting Notes
SHARPn Summit Announced
- April 2012
Building solutions that matter
- Enabling secondary use of EHR data to generate new
- knowledge, improve care, and address population needs
This year the SHARPn face-to-face will be expanded to include the stakeholder community for a Summit on:
- Standards, Data Integration & Semantic Interoperability
- Natural Language Processing
- Phenotyping: clinical trial selection, clinical decision support, quality measurement
- Software evaluation
Stakeholders are being invited to attend to:
- Learn more about SHARPn and the health IT field
- Explore technologies and tools that enable secondary uses of EHR data
- Participate in a hands-on tutorial from experts on how to better leverage secondary data using open source tools
- Present your paper or poster on related topics through a peer reviewed process
- Work side-by-side with community leaders to develop and refine customer and stakeholder requirements
Please join us in Rochester, MN June 11-12. The meeting will include tutorials, published paper and poster presentation, technical demos and code-a-thon opportunities. Meeting registration is free, and breakfast and lunch will be provided for registered attendees.
cTAKES 2.5 released
- May 2012
The SHARP (SHARPn) Natural Language Processing (NLP) team has released an updated version (2.5) of the Clinical Text Analysis and Knowledge Extraction System (cTAKES). cTAKES is a free and open source NLP system for accessing clinical information stored in free text through NLP techniques.
- cTAKES 2.5 includes
- a new attributes (assertion) extractor
- a semantic role labeler
- an additional sectionizer
- updates to the coreference resolver
- and an updated part-of-speech model
Multiscrubber Release
- November 22,2011
A meta-classifier approach to de-identification is released.
SHARPn Attends AMIA 2011
- November 2012
SHARPn Collegues are attending AMIA with a strong showcase of presentations, papers and posters.
Introducing cTAKES 1.2.2 and NEW integrated version icTAKES
- October 20, 2011
The Mayo SHARP (SHARPn) Natural Language Processing (NLP) team is excited to announce an updated release of the Clinical Text Analysis and Knowledge Extraction System (cTAKES), cTAKESv1.2. cTAKES is a free and open source NLP system distributed by Mayo Clinic through Open Health Natural Language Processing (OHNLP) consortium which allows researchers to utilize clinical information stored in free text through NLP techniques.
cTAKES release 1.2 includes a new annotator (beta version), SideEffect, which extracts physician-asserted drug side effects from clinical notes. This release also introduces an integrated version of cTAKES, icTAKES, which provides an integrated version of cTAKES for end users and developers. To distinguish these two cTAKES versions, cTAKES is distributed as cTAKES1.2.1 and icTAKES is distributed as cTAKES1.2.2.
https://wiki.nci.nih.gov/x/fYDQAw
Clinical NLP Evaluation Workbench
- October 17, 2011
SHARPn NLP team is excited to announce the release of Clinical NLP Evaluation Workbench ( http://orbit.nlm.nih.gov/resource/clinical-nlp-evaluation-workbench). The intended audiences of the tool are NLP researchers and developers.
International Consensus Bearing to SHARPn
- October 2011
Stan Huff introduces International consensus group with Detailed Clinical Models, Clinical Information Modeling Initiative (CIMI)
- Archetype Object Model/ADL 1.5 openEHR
- CEN/ISO 13606 AOM ADL 1.4
- UML 2.x + OCL + healthcare extensions
- OWL 2.0 + healthcare profiles and extensions
- MIF 2 + tools HL7 RIM – static model designer
https://csfe.aceworkspace.net/sf/projects/clinical_information_modeling_in
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