Accessing Digital Information

Douglas MacFadden

April 30, 2014

Harvard Catalyst and The Countway Medical Library and CBMI at Harvard Medical School

Deputy Director Informatics Program andChief Informatics Officer, Harvard Catalyst

Overview

Countway Library• Established 1875• One of the largest medical libraries in the world• Serves Harvard Medical School and investigators at any of it’s 17 affiliated

hospitals

Center for Biomedical Informatics• Established 2005• Links the library with biomedical informatics research

Harvard Catalyst• Established in 2008• Funded from the NIH as part of the Clinical Translational Science Awards

program• Renewed funding in 2013

Themes Connecting the Work

Accessing Information• Content Portals• Content Curation• Ontology Development

Sharing and Collaboration• Resources• People• Data

Supporting Education• Just in time workshops• Video capture of live classes• Online learning

Countway Library and the Center for Biomedical Informatics

The Francis A. Countway Library of Medicine, one of the largest medical libraries in the world, serves the Harvard Medical School, Harvard School of Public Health, Harvard School of Dental Medicine, Boston Medical Library and the Massachusetts Medical Society. The Countway Library holds more than 630,000 volumes, subscribes to 3,500 current journal titles and houses over 10,000 non-current biomedical journal titles. The library also houses one of the world's leading medical history collections, and provides access to many electronic information resources.

The Center for Biomedical Informatics (CBMI) at Harvard Medical School (HMS) conducts informatics research with a strong emphasis on translational science informed by innovative computational strategies.

Directors:• Isaac Kohane, MD, PhD

Henderson Professor of Pediatrics and Health Sciences and TechnologyCo-Director Center for Biomedical Informatics Harvard Medical SchoolDirector of the Francis A. Countway Library of Medicine

• Alexa T. McCray, PhDAssociate Professor of MedicineCo-Director Center for Biomedical InformaticsAssociate Director of the Francis A. Countway Library of Medicine

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Countway Portal

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Center for Biomedical Informatics

Center for History of Medicine: Collections

Medical Heritage LibraryCenter for History of Medicine collaboration with the Internet Archive, The Augustus C. Long Health Sciences Library at Columbia University and Columbia University

Libraries/Information Services, The College of Physicians of Philadelphia The Cushing/Whitney Medical Library at Yale University, The Francis A. Countway Library of Medicine at Harvard University, National Library of Medicine, The New York Academy of Medicine The Welch Medical Library, Library of the Institute of the History of Medicine, and the Alan Mason Chesney Medical Archives of the Johns Hopkins Medical Institutions Wellcome Library

Community Connect to Research

Improving understanding of health research

Mobile Health Map

Fostering a mobile care delivery and research community in collaboration with Dr. Nancy E. Oriol, Dr. Anthony Vavasis and the Mobile Health Clinics Network

Autism Ontology

Providing Tools for Semantically Rich Information Representation

Harvard University Library Collaborations

EAS/EASi: Electronic Archiving System• EAS is the Electronic Archiving System, which along with EASi, its User

Interface (UI) for archivists, is a prototype system being developed in LTS for archiving electronic content at Harvard. Initially, the system is being designed to permit ingest, archival processing and transfer to the Digital Repository Service (DRS) for long term preservation of email. In the future, the system will accommodate additional born-digital formats.

Library Cloud: provides access (API) to Harvard Library data• LibraryCloud is a metadaserver. It makes information about the content and

usage of Harvard Library items available for use by applications developed by anyone.

LibLab Projects

Blink: Linked open data, expanded authority search capabilities, and synonym expansion• Convert existing MARC records to RDF in order to use Linked Open Data and

synonym enhancement through a query rewriting web-service to improve access and discoverability to the Countway Digital Library, and to enhance LibraryCloud and the DPLA platform.

ASHE: Automatic Subject Heading Extraction• This project utilizes proven techniques in term and concept extraction for the

automatic recognition of subject headings in library written materials. Project will improve the completeness of existing catalog records and provide an opportunity to novel experimentation.

More Information about Countway and CBMI

• Countway Portal: https://www.countway.harvard.edu/• CBMI: https://cbmi.med.harvard.edu/• CHoM Collections: http://collections.countway.harvard.edu/onview/• Strong Medicine: http://collections.countway.harvard.edu/onview/collections/show/94• Community Connect to Research: http://www.connecttoresearch.org/• Medical Heritage Library: http://www.medicalheritage.org/• Mobile Health Map: http://www.mobilehealthmap.org/• ASHE: https://osc.hul.harvard.edu/liblab/proj/automatic-subject-heading-extraction• BLINK:

https://osc.hul.harvard.edu/liblab/proj/blink-linked-open-data-expanded-authority-search-capabilities-and-synonym-expansion

• EAS/EASi: http://hul.harvard.edu/ois/systems/eas/• Autism Ontology: https://bioportal.bioontology.org/ontologies/ASDPTO• Library Cloud: http://librarycloud.harvard.edu/

Harvard CatalystFounded in 2008, the Harvard Clinical and

Translational Science Center supports an academic home that creates an integrated research and training environment across Harvard Medical School and its partner institutions in order to improve human health. It provides and/or creates access to resources and services to support all steps across the full spectrum of clinical and translational research, and facilitates the training and career development of the translational research workforce.

Harvard Catalyst is one of 60 centers funded by the NIH under NCATS, the National Center for Advancing Translational Sciences. In additional to NIH funding, Harvard Catalyst is supported by 17 Harvard-affiliated hospitals and works in partnership with all 11 Harvard schools. In 2013, Harvard Catalyst was awarded a second five-year grant.

Principle InvestigatorLee Nadler, MD

Dean for Clinical and Translational Research, Harvard Medical SchoolVirginia and D.K. Ludwig Professor of Medicine, Dana Farber Cancer Institute

Resources for Investigators

Harvard Catalyst makes available the following resources for Harvard-affiliated researchers:

• Consultations (biostatistics, bioinformatics, regulatory)• Education (currently 13 courses)• Pilot funding opportunities: provided grants to hundreds of

investigators to form inter-institutional teams as they collaborate on interdisciplinary research projects in areas such as childhood obesity, health disparities in cancer, novel utilization of SHRINE, innovative methodologies in imaging, and Type 1 diabetes.

• Clinical research services at affiliated hospitals• Informatics tools

Additional Harvard Catalyst Initiatives and Programs

• Diversity: The Program for Faculty Development and Diversity has impacted the culture at HMS through its mentorship programs, faculty fellows (all of which have received promotions), visiting research interns (boasting 23 alumni), and summer clinical and translational research interns (43 alumni).

• Community: The Population Health Research Program has facilitated partnerships with health departments and communities to translate evidence into policy, track policy implementation, link data systems, and evaluate policy changes.

• Health Disparities: The Health Disparities Research Program convened a Harvard-wide symposium on this research area, while a May 2012 conference focused on sleep disparities. Their co-sponsored 2012-13 Gene-Environment Disparities Research workshop series has featured renowned presenters working across these disciplines.

Leading Efforts to Improve the Health of NFL Players

In February 2014, Harvard Catalyst began leading the NFLPA/Harvard Accelerated Research Collaboration to Protect and Improve the Health of Football Players. This multi-million award from the National Football League Players Association (NFLPA) is funding a 7-year initiative led by a highly diverse and integrated team of Harvard investigators. The initiative presents an opportunity to work with leading experts across Harvard University and partnering institutions across the U.S.

Harvard Catalyst Informatics

Lower barriers to research• SHRINE: discovery and analysis of patient clinical data• Profiles: discovery of potential collaborators• eagle-i: discovery of cores and developed resources• REDCap: support and training for the Vanderbilt electronic data capture tool

Partner with other HC programs to build and support informatics tools that implement new policy across institutions and improve efficiency:• IRB Cede Review workflow• CRC Protocol Review workflow• CRC Scheduling workflow• Education Course Compendium and Video Library

Provide just-in-time informatics training to all members of the research communityAccess to all Harvard Catalyst resources, services and educational offerings via web portal

SHRINE: Shared Health Research Information Network

Software and policy to build networks of patient data for research. Developing support for clinical trial recruitment.

Harvard network of 5 competing hospitals

Open Source• Annual Conference• Carranet registry for rare

pediatric Conditions (60 hospitals)

• UC Rex research and quality of care across the UC system

• CCHMC led pediatric registry

• HOMERUN quality of care• National Demonstration

network of 8 sites• PCORI• NIH NCATS CTSA

Profiles

Broadly Implemented & NetworkedVIVO Ontology and Plug-In SupportLinked Open Data

eagle-i

Search for Core Labs in eagle-i National network for discovery of biomedical resources

• Over 90,000 resources

• Over 500 cores• 18 ontology

collaborations• 27 sites & growing

Collaboration with transaction facilitators (e.g. Science Exchange, AddGene, DSHB)

REDCap Support and Training

Produced by Vanderbilt• REDCap is a secure, web-based application for building and

managing online surveys and databases

HMS is the second largest REDCap site

CRC Protocol Review and Scheduling

• Decrease time and effort for investigators through web based workflow• Support more comprehensive research due to multi-institutional support• Software is available for sharing as open source

Education Support

Comprehensive services for Education, including:• Course Compendium searchable database with flexible metadata support• Video capture, production (including copyright redaction process) and online

library

IRB Cede Review

• IRB Cede Review Form streamlines multi-site human studies by eliminating the need for duplicative IRB reviews across the diverse, multi-institutional Harvard community.

• Policy and software are available for sharing with other CTSA sites.

Informatics just-in-time training

27 different bioinformatics workshops offered repeatedly throughout the year including:

• Genome resources• Statistics• Microarrays and Gene Expression including transcription factor analysis• Pathway analysis• MicroRNA’s analysis• Protein engineering• Sequencing analysis (mRNA-Seq and Exome Sequencing)• Human Genome databases (Human Gene Mutation Database• NIH’s tools including Gene Omnibus Database and UCSC Genome Browser)• Programming topics like Bioperl and Perl for biological text mining

Harvard Catalyst Web Portal

Domain Specific Portals

Integrating domain focused:• Content• Events• People• Resources

Sites:• Immunology• Center for Primary

Care

Open source: open.med

More Information about Harvard Catalyst

• Harvard Catalyst Portal: http://catalyst.harvard.edu/

• Open.med: https://open.med.harvard.edu/

• Immunology: https://immunology.hms.harvard.edu/

• Center for Primary Care: https://primarycare.hms.harvard.edu/

Questions?