SHARP Project Wiki:Current events

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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

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.

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.

Phenoportal Presentation

HIMSS 2013

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

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.

SHARPn Member Sessions

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


President Barack Obama has declared the week of September 11-16, 2011, National Health Information Technology Week.

September 2011

National Health Information Technology Week is a time to highlight the importance of efficient information systems that protect the privacy and security of personal health information while improving the delivery of health care in the United States.

There is no better time for the health information technology (health IT) community to come together to raise national awareness regarding the consistent breakthroughs and hard work industry professionals, providers, and consumers put forward on a daily basis to ensure they are moving toward the common goal of advancing the future of health care through private and secure health IT.

Learn more about health IT by visiting HealthIT.gov.

HealthITWeekLogo

SHARPn Tracer-Shot Pilot

{{#ev:youtube|a3VWPayw2Bc}} SHARPn Pilot Calvin Beebe; SHARPn Chief Architect; Senior Technical Specialist at Mayo Clinic discusses the 'tracer-shot' pilot conducted in the SHARPn program where deidentified data from Intermountain Healthcare and Mayo Clinic was run through a pilot to normalize the data in a comparable and consistent manner for which secondary use information could be derived.

SHARP Area 4 Face-to-Face Conference Held - June 30 & July 1, 2011

July 2012
Agenda & Presentations
http://informatics.mayo.edu/sharp/index.php/Main_Page/FacetoFace_2011

SHARP 2011b.jpg

Face to Face Group Photo July 1, 2011

Introducing cTAKES 1.3.2

December 23, 2011

An updated release of the Clinical Text Analysis and Knowledge Extraction System (cTAKES) is now available, cTAKES 1.3.2.

This update now allows inclusion of a set of UMLS dictionaries (SNOMED-CT and RxNorm). The Dictionary Lookup component now includes these dictionaries for doing SNOMED CT and RxNorm Named Entity Recognition out-of-the-box. You no longer need to take an extra step to get production level dictionaries except to supply a UMLS username and password. As well, two new annotators--Constituency Parser and Coreference resolver are included in this new release.

https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/CTAKES_1.3

Announcing launch of Cloud Computing Environment

December 2011
  • The SHARPn cloud computing environment, also known as "the cloud" is proudly constructed by the SHARPn infrastructure team and is basically a set of virtual machine images that can be instantiated, used, and shut down for Secondary Use of EHR Data research. Secondary Use of EHR Data is the focus of SHARPn, AREA 4 and this web site. The software developed by SHARPn will allow researchers and clinicians to pull together very different types of healthcare data and ask questions about disease, prevention, outcomes, and care delivery. Answering these questions requires a robust, high-quality dataset which can be generated by software in the SHARPn cloud computing environment.
  • Within the cloud computing environment there are four building blocks ...
    • Clinical Data Normalization Services and Pipelines
    • Natural Language Processing
    • High Throughput Phenotyping
    • Scaling Capacity

The SHARP Area 4 NLP team announces new annotator

  • The SHARP 4 NLP team would like to announce the release of a new annotator in cTAKES. This is the second cTAKES release from efforts completed through the ONC-funded SHARP project.
  • This release includes a Smoking Status Classifier that processes clinical documents and identifies patients' smoking status at the patient level as well as the document level. This pipeline will generate one of five smoking status categories:
    • Past smoker
    • Current smoker
    • Smoker
    • Non-smoker
    • Unknown

The Meaningful Yoose Rap

Trying to figure out what eligible providers have to do to receive incentive payments from CMS for the meaningful use of electronic health records? Everything you need to get started is right here, delivered in under three minutes!

The American College of Medical Informatimusicology Proudly Presents: The Meaningful Yoose Rap, Written and Performed by Dr. HITECH

SHARP Area 4 - Offers Roundtable for Cloud-Deployed Clinical Natural Language Processing

May 22-24, 2011
  • Seattle, WA

This roundtable brings together nationally-recognized experts in information security, key stakeholders from health care and research institutions, and representatives of leading cloud service providers to identify legal, regulatory, technical and governance prerequisites for secure, regulatory-compliant processing of patient clinical information in externally-hosted computing environments ("the cloud").

SHARP Area 4 - Visits HIMSS 11 Feburary 2011

February 2011

Lacey Hart Dr. Chute Wil Yu SHARP Program Managers

SHARP Area 4 - Leverages "Deep Question Answering" of UIMA

February 2011

Out of the IBM TJ Watson Research Lab, represents a major advance in what is called “Deep Question Answering” technology – the ability of a computer to do something that’s far more challenging than chess: to understand natural human speech about a limitless range of topics, and to make informed judgments about them. Watson expects the science to elevate computer intelligence; to take human-to-computer communication to new levels; and to help extend the power of advanced analytics to make sense of vast quantities of structured and unstructured data. Watson on Healthcare

For example, the Deep QA technology could, in the not so distant future, provide critical, timely information to physicians to help diagnose and treat patients. In SHARP Area 4 the UIMA-AS technology framework will be the backbone of the various tools and architecture. Initial practice use cases will be piloted in the SEMN Beacon.

{{#ev:youtube| tpv03YfhRlc }} UIMA in SHARPn Program: Marshall I. Schor, SHARPn Co-Investigator-Apache UIMA framework; Senior Technical Staff at TJ Watson Research Lab, IBM; Marshall describes the use of IBM Research: Unstructured Information Management Architecture (UIMA) in the SHARPn program.

IBM and the Jeopardy! Challenge Jeopardy! The IBM Challenge will reveal just how far IBM researchers have pushed the boundaries of these technologies.

  • PBS’ NOVA Pproduced a new film on artificial intelligence with unique access to IBM's Watson and the machine's bid to ocompete on Jeopardy! NOVA’s “Smartest Machine On Earth” Premiered February 9, 2011 on PBS.
  • Jeopardy! matches aired February 14, 15, and 16.

In case you missed the matches on television, watch this video for a re-cap of the action, reactions from the competitors and reflections by the research team as they look toward the future.

Why Jeopardy Image

New cTAKES Annotator Now Available.

March 14, 2011

The SHARP 4 NLP team is excited to announce the release of a new annotator in cTAKES. This is the second cTAKES release from efforts completed through the ONC-funded SHARP project.

This release includes a Smoking Status Classifier that processes clinical documents and identifies patients’ smoking status at the patient level as well as the document level. This pipeline will generate one of five smoking status categories: past smoker, current smoker, smoker, non-smoker and unknown.

This annotator is modular, so if you already have cTAKES installed you can add this piece without having to re-install cTAKES.

Click here to download: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/OHNLP_Documentation_and_Downloads

The SHARP Area 4 NLP team is excited to announce the release of cTAKES 1.1.

December 22, 2010
  • This is the first cTAKES release from efforts completed through the ONC-funded SHARP project.
  • The new software includes an updated medication annotator that will allow researchers to extract drug mentions from clinical free text. This was first developed under a grant from the AT&T Foundation. It includes features such as: Frequency; Dosage; Strength; Form; Route; Duration; Drug change status.
  • This version of cTAKES also includes a dependency parser — a foundational component that analyzes syntactic structure. This building block enables the development of future cTAKES components that utilize grammatical context to extract events, attributes, and relations from clinical documents.
  • Click here to download: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/OHNLP_Documentation_and_Downloads
  • Stay tuned. The team is working on more updates to cTAKES that will advance the secondary use of Electronic Health Record data.

Government report on Healthcare Information Technology

December 8, 2010

The President's Council of Advisors on Science and Technology (PCAST) released a report entitled “Realizing the Full Potential of Health Information Technology to Improve Healthcare for Americans: The Path Forward.” http://www.whitehouse.gov/administration/eop/ostp/pcast/docsreports

Dr. Friedman visits with Mayo Clinic

September 3, 2010

Dr. Friedman visits with Mayo Clinic leaders and the SHARP Area 4 program team.

Area 4: Program Progress Presentation

SHARP Area 4 is proud to announce a Clinical Element Model (CEM) Search Tool

August 23, 2010
Practical Modeling Issues
Stanley Huff
Website: http://www.clinicalelement.com/

Minnesota e-Health Summit 2010

June 16-17, 2010

The purpose of the Summit is to provide participants with tools and resources to guide success in implementing EHRs and HIT in the current economic climate. The 2010 e-Health Summit keynote features Dr. David Blumenthal, the National Coordinator for Health Information Technology, who is leading the national effort for adoption and meaningful use of health IT. Other highlights include:

SHARP Research and Beacon Community Collaborative: Christopher G. Chute, MD, DrPH, Mayo Clinic (pdf 638Kb/ 6pgs)

SHARP Area 4 Face-to-Face Conference Held - June 21-22, 2010

Agenda & Presentations
http://informatics.mayo.edu/sharp/index.php/2010_Face-to-Face_Meeting
Face to Face Group Photo June 22,2010
Face to Face Group Photo June 22,2010

Healthcare IT News - Sebelius heads to Mayo Clinic for news conference

June 2, 2010

ROCHESTER, MN – Health information technology will top the agenda at the Mayo Clinic Thursday morning at a news conference led by Health and Human Services Secretary Kathleen Sebelius. U.S. Sens. Amy Klobuchar and Al Franken; U.S. Reps. Tim Walz, Betty McCollum and Ron Kind; and Mayo Clinic President and CEO, John Noseworthy MD, will join Sebelius to highlight Mayo Clinic's patient-centered, high-value care approach as well as its health information technology efforts.

Mayo Clinic, recognized by The Leapfrog Group as one of the best health systems in the country, is known as a leader on the information technology front. The Mayo Clinic College of Medicine in Rochester, Minn., recently received a $12.2 million Beacon Community grant, one of 15 federal grants awarded to communities and organizations across the country to serve as models for healthcare IT use. Mayo Clinic will use the grant on work to enhance patient management and to reduce costs associated with hospitalization and emergency services for patients with diabetes and childhood asthma. It will also work to reduce health disparities for underserved populations and rural communities.

Mayo Clinic also received $15 million from the federal SHARP program (Strategic Health IT Advanced Research Projects) to study the secondary use of EHR data. It aims to develop strategies to make use of data that will be stored in EHRs to improve the overall quality of healthcare, while maintaining data privacy and security.

Mayo Clinic is partnered with GE Healthcare and Intel on a yearlong study evaluating the benefits of remote monitoring devices for home-based patient care.

Recently Mayo Clinic announced it would integrate Mayo Clinic EmbodyHealth, a personal health management portal, with the Dossia Personal Health Platform.

ISO 16223/HL7 Initiated "Standards Convergence" Proposal announced

May 13, 2010

Read more.

Potential for SHARP research

April 8, 2010

Modernhealth.com - Friedman sees big potential in SHARP research

In just a couple of years, the Office of the National Coordinator for Health Information Technology at HHS will be looking for tangible results from the $60 million in public investment that the ONC has made in the Strategic Health IT Advanced Research Projects.

Charles Friedman, chief scientific officer at the ONC, also expects the unanticipated will emerge from the research and development program, called SHARP for short.

“You never know what's going to result from what you fund directly, but I can tell you now, the synergies have an enormous chance of paying dividends above and beyond the funding of these groups,” Friedman said. “The coalitions that are being formed through SHARP will yield these benefits beyond even the work being funded.” READ MORE

SHARP Awards

April 2010

HIMSS News - ONC Announces SHARP Awards: A Look at Secondary Use of EHR Data Research By Christopher G. Chute, MD, DrPH

The Office of the National Coordinator for Health Information Technology (ONC) awarded $60 million in research grants through the Strategic Health IT Advanced Research Projects (SHARP) Program to the Mayo Clinic College of Medicine, Harvard University, University of Texas Health Science Center at Houston and University of Illinois at Urbana-Champaign. The Mayo Clinic College of Medicine, on behalf of a consortium of several entities, proposed research that will generate a framework of open-source services which can be dynamically configured to transform EHR data into standards-conforming, comparable information suitable for large-scale analyses, inference and integration of disparate health data.

These services will be applied to phenotype recognition (disease, risk factor, eligibility or adverse event) in medical centers and population-based settings. Finally, we examine data quality and repair strategies with real-world evaluations of their behavior in Clinical and Translational Science Awards (CTSAs), health information exchanges (HIEs) and Nationwide Health Information Network (NHIN) connections.

The Mayo-led consortium has assembled a federated informatics research community committed to open-source resources that can industrially scale to address barriers to the broad-based, facile and ethical use of EHR data for secondary purposes. We will collaborate to create, evaluate and refine informatics artifacts that advance the capacity to efficiently leverage EHR data to improve care, generate new knowledge and address population needs. Our goal is to make these artifacts available to the community of secondary EHR data users, manifest as open-source tools, services and scalable software. In addition, we have partnered with industry developers who can make these resources available with commercial deployment.

We propose to assemble modular services and agents from existing open-source software to improve the utilization of EHR data for a spectrum of use-cases and focus on three themes:

  • Normalization
  • Phenotypes
  • Data Quality/Evaluation

Our six projects span one or more of these themes, including:

  • Semantic and Syntactic Normalization
  • Natural Language Processing (NLP)
  • Phenotype Applications
  • Performance Optimization
  • Data Quality Metrics
  • Evaluation Frameworks

Each of these services will have open-source deployments as well as commercially supported implementations.

Christopher G. Chute, MD, DrPH, established the Division of Biomedical Informatics at Mayo Clinic, overseeing a program of applied research and development focusing upon clinical and genomic data sources, management, standardization and interpretation.

NOTE: This article appeared in the April 2010 issue of HIMSS Clinical Informatics Insights.

Mayo Clinic and the SHARP grant

April 06, 2010

Mayo Clinic Awarded Major Health Information Technology Grant

ROCHESTER, Minn. — Citing Mayo's ability to translate research and innovation into medical practice, the U.S. Department of Health and Human Services has named Mayo Clinic as one of four institutions to receive a significant research grant as part of the Strategic Health IT Advanced Research Projects (SHARP) program. Mayo will receive $15 million as part of an overall $60 million awarded. Other awardees include Harvard University, the University of Texas Health Science Center and the University of Illinois.

Mayo's role will be to research and advance methods for using electronic medical records for such additional purposes as medical research, while also "maintaining privacy and security." Mayo has been a pioneer in adopting the electronic medical record (Mayo has had paperless records since 2005) and an innovative leader in using medical records to advance research.

"This is a great recognition of Mayo's leadership in this area and this award will allow us to develop methods so we effectively share this approach with others," says Christopher Chute, M.D., Dr. P.H., Mayo principal investigator.

The government announcement says the research will involve interdisciplinary efforts among researchers, health care providers and the technology industry. The goal is to integrate findings into medical practice quickly across the nation.

"This is not ivory tower research," says David Blumenthal, M.D., national coordinator for Health Information Technology. "Its goal is to quickly infuse the dynamic health IT sector with new thinking, ideas and solutions."

"There's a clear need for progressive and innovative thinking to overcome barriers and ensure the long-term viability of our health care system," says Dr. Blumenthal.

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About Mayo Clinic

Mayo Clinic is the first and largest integrated, not-for-profit group practice in the world. Doctors from every medical specialty work together to care for patients, joined by common systems and a philosophy of "the needs of the patient come first." More than 3,700 physicians, scientists and researchers, and 50,100 allied health staff work at Mayo Clinic, which has campuses in Rochester, Minn; Jacksonville, Fla; and Scottsdale/Phoenix, Ariz.; and community-based providers in more than 70 locations in southern Minnesota., western Wisconsin and northeast Iowa. These locations treat more than half a million people each year. To obtain the latest news releases from Mayo Clinic, go to www.mayoclinic.org/news. For information about research and education, visit www.mayo.edu. MayoClinic.com (www.mayoclinic.com) is available as a resource for your health stories

December 18, 2009

Keeping a SHARP Focus on Innovation

David Blumenthal, M.D., M.P.P. National Coordinator for Health Information Technology U.S. Department of Health & Human Services

Today the Obama administration announced the availability of $60 million in Recovery Act funds to support the development of the Strategic Health IT Advanced Research Projects (SHARP) program. SHARP awards will fund research focused on identifying technology solutions to address well-documented problems impeding broad adoption of health information technology (health IT). By helping to overcome key challenges, the research will also accelerate progress towards achieving nationwide meaningful use of health IT.

As we continue this unprecedented effort towards meaningful use and seamless, secure information exchange, we also must acknowledge that there remains a gap between the promise of health IT and the realization of its full benefits. To achieve the goal of a transformed health care delivery system, it’s critical that we close this gap by enabling a robust research infrastructure that can focus on areas where “breakthrough” advances are needed to help clear obstacles to adoption. Under the SHARP program, four awardees will receive funding to develop multidisciplinary research projects that will identify such breakthrough solutions.

SHARP program awardees will create research programs that draw from many areas of expertise. They will focus on issues of central interest to all health IT stakeholders, fostering considerable discussion and debate. If for example, SHARP research helped identify new methods to create tools that will, through their incorporation into deployed technology, enhance data security, then public trust in the electronic maintenance and exchange of health information would be reinforced and strengthened – which would in turn help encourage broader adoption.

Areas requiring this innovative research approach that will be tackled by the SHARP awardees include the security of health IT, patient-centered cognitive support, application and network platform architectures, and the secondary use of EHR data as a way of measuring and improving quality of care.

Another important aspect of the SHARP program is that the research projects will bring together key stakeholders – researchers, patient groups, health care providers, and others – to work with one another to transform health IT research into applications. This collaborative approach allows us to consider the many voices of health IT stakeholders, and work together towards common goals. With our eyes on the vision of patient-centered, quality health care we can focus research on innovative, pragmatic, and realistic solutions, which can then be implemented across the nation.

I truly look forward to seeing the innovative research that emerges from this program. I know that this research will provide critical insights that will bring us closer every day to a better, more efficient health care delivery system, enabled by health IT and empowered by the seamless and secure exchange of electronic health information.


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