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Accessing Digital Information
Douglas MacFadden
April 30, 2014
Harvard Catalyst and The Countway Medical
Library and CBMI ...
Overview
Countway Library
• Established 1875
• One of the largest medical libraries in the world
• Serves Harvard Medical ...
Themes Connecting the Work
Accessing Information
• Content Portals
• Content Curation
• Ontology Development
Sharing and C...
Countway Library and the Center for
Biomedical Informatics
The Francis A. Countway Library of Medicine, one of the largest...
Countway Portal
Date here Footer here 5
Center for Biomedical Informatics
Center for History of Medicine: Collections
Medical Heritage Library
Center for History of Medicine collaboration with the Internet Archive, The Augustus C. Long Heal...
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. An...
Autism Ontology
Providing Tools for Semantically Rich Information Representation
Harvard University Library Collaborations
EAS/EASi: Electronic Archiving System
• EAS is the Electronic Archiving System, ...
LibLab Projects
Blink: Linked open data, expanded authority search capabilities, and
synonym expansion
• Convert existing ...
More Information about Countway and CBMI
• Countway Portal: https://www.countway.harvard.edu/
• CBMI: https://cbmi.med.har...
Harvard Catalyst
Founded in 2008, the Harvard Clinical and
Translational Science Center supports an
academic home that cre...
Resources for Investigators
Harvard Catalyst makes available the following
resources for Harvard-affiliated researchers:
•...
Additional Harvard Catalyst Initiatives and
Programs
• Diversity: The Program for Faculty Development and Diversity has
im...
Leading Efforts to Improve the Health of NFL Players
In February 2014, Harvard Catalyst began leading the
NFLPA/Harvard Ac...
Harvard Catalyst Informatics
Lower barriers to research
• SHRINE: discovery and analysis of patient clinical data
• Profil...
SHRINE: Shared Health Research Information Network
Software and policy to build
networks of patient data for
research. Dev...
Profiles
Broadly Implemented & Networked
VIVO Ontology and Plug-In Support
Linked Open Data
eagle-i
Search for Core Labs in eagle-i National network for
discovery of biomedical
resources
• Over 90,000
resources
• O...
REDCap Support and Training
Produced by Vanderbilt
• REDCap is a secure, web-based application for building and
managing o...
CRC Protocol Review and Scheduling
• Decrease time and effort for investigators through web based workflow
• Support more ...
Education Support
Comprehensive services for Education, including:
• Course Compendium searchable database with flexible m...
IRB Cede Review
• IRB Cede Review Form streamlines multi-site human studies by eliminating the
need for duplicative IRB re...
Informatics just-in-time training
27 different bioinformatics workshops offered repeatedly throughout the year
including:
...
Harvard Catalyst Web Portal
Domain Specific Portals
Integrating domain
focused:
• Content
• Events
• People
• Resources
Sites:
• Immunology
• Center f...
Open source: open.med
More Information about Harvard Catalyst
• Harvard Catalyst Portal: http://catalyst.harvard.edu/
• Open.med: https://open.m...
Questions?
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Harvard Catalyst works with Harvard schools and affiliated hospitals to build an environment where discoveries are rapidly and efficiently translated to improve human health

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APLIC 2014 - Douglas MacFadden on Harvard Catalyst

  1. 1. 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 and Chief Informatics Officer, Harvard Catalyst
  2. 2. 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
  3. 3. 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
  4. 4. 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 Technology Co-Director Center for Biomedical Informatics Harvard Medical School Director of the Francis A. Countway Library of Medicine • Alexa T. McCray, PhD Associate Professor of Medicine Co-Director Center for Biomedical Informatics Associate Director of the Francis A. Countway Library of Medicine 4
  5. 5. Countway Portal Date here Footer here 5
  6. 6. Center for Biomedical Informatics
  7. 7. Center for History of Medicine: Collections
  8. 8. Medical Heritage Library Center 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
  9. 9. Community Connect to Research Improving understanding of health research
  10. 10. 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
  11. 11. Autism Ontology Providing Tools for Semantically Rich Information Representation
  12. 12. 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.
  13. 13. 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.
  14. 14. 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/
  15. 15. Harvard Catalyst Founded 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 Investigator Lee Nadler, MD Dean for Clinical and Translational Research, Harvard Medical School Virginia and D.K. Ludwig Professor of Medicine, Dana Farber Cancer Institute
  16. 16. 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
  17. 17. 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.
  18. 18. 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.
  19. 19. 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 community Access to all Harvard Catalyst resources, services and educational offerings via web portal
  20. 20. 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
  21. 21. Profiles Broadly Implemented & Networked VIVO Ontology and Plug-In Support Linked Open Data
  22. 22. 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)
  23. 23. 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
  24. 24. 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
  25. 25. 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
  26. 26. 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.
  27. 27. 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
  28. 28. Harvard Catalyst Web Portal
  29. 29. Domain Specific Portals Integrating domain focused: • Content • Events • People • Resources Sites: • Immunology • Center for Primary Care
  30. 30. Open source: open.med
  31. 31. 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/
  32. 32. Questions?

Harvard Catalyst works with Harvard schools and affiliated hospitals to build an environment where discoveries are rapidly and efficiently translated to improve human health

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