National Library of Medicine Strategic Plan RFI

screenshot-2016-11-11-11-14-35Dr. Patricia Flatley Brennan, the new Director of the National Library of Medicine (NLM), recently visited OHSU to celebrate the 25th Anniversary of the BICC. During her plenary presentation, she outlined her vision for the third century of NLM. Now, she and her colleagues are seeking your input on the NLM Strategic Plan. Everyone is encouraged to respond, with particular emphasis on four roles:


  1. Role of NLM in advancing data science, open science, and biomedical informatics
  2. Role of NLM in advancing biomedical discovery and translational science
  3. Role of NLM in supporting the public’s health: clinical systems, public health systems and services, and personal health
  4. Role of NLM in building collections to support discovery and health in the 21st century

In the following areas:

  1. Identify what you consider an audacious goal in your area of interest – a challenge that may be daunting but would represent a huge leap forward were it to be achieved.  Include input on the barriers to and benefits of achieving the goal.
  2. The most important thing NLM does in this area, from your perspective.
  3. Research areas that are most critical for NLM to conduct or support.
  4. Healthcare systems and public health arenas in which NLM participation is most critical.
  5. New data types or data collections anticipated over the next 10 years.
  6. Other comments, suggestions, or considerations, keeping in mind that the aim is to build the NLM of the future.


Celebrating 25 years of fueling medical advancement with information

BICC anniversary, celebration, event

OHSU celebrated 25 years of the Biomedical Information Communication Center on Oct. 28, telling a story about progress by tracing the evolution of programs and resources that the BICC, as it’s now called, has housed since it was built in 1991.

“It’s important to take these moments to understand and celebrate how we became what we are and to consider how that history should inform our future,” said William Hersh, M.D., professor and chair of medical informatics and clinical epidemiology, OHSU School of Medicine. “I’m grateful to our local and national leaders and faculty, past and present, who were willing to come to help us do this.”

Late Senator Mark Hatfield key to BICC birth

The BICC was built through the federal Integrated Advanced Information Management System initiative, which sought to springboard the management of information into a new era.

But the actual birth of the BICC came about in a uniquely Oregon way, through the earmarking prowess of the late Senator Mark Hatfield, whose visionary use of this funding mechanism transformed OHSU’s landscape in the 1980s and 1990s. Hatfield added the IAIMS appropriation for the BICC to the National Library of Medicine budget.

BICC anniversary, celebration, eventWhile this funding approach was viewed unfavorably by some in academic medicine and invited additional scrutiny from the National Library of Medicine, it resulted in a great deal of productive planning and 25 years of research, education and services for the OHSU community and beyond.

“The key to the success of the BICC was the energy and enthusiasm of the people who worked to plan innovative library services and launch one of the earliest health informatics programs in the country,” said Chris Shaffer, associate professor and University Librarian. “The BICC represented a great leap forward into the information future for OHSU.”

Celebration book-ended by history

Recognizing the link between the BICC and the National Library of Medicine, the day of celebration was bookended with talks by Dr. Donald Lindberg, the retired NLM director who led the Integrated Advanced Information Management System initiative and spoke at the BICC dedication in November 1991, and new NLM Director Dr. Patricia Brennan, a nurse informaticist. In between, faculty and leaders past and present filled out the history of the work the BICC has supported from early telemedicine initiatives to a partnership between DMICE and the Library to develop Big Data to Knowledge (BD2K) open educational resources.

Speakers who helped frame past work and accomplishment of the BICC included:

  • David Witter, M.A. – former Interim President of OHSU
  • David Hickam, M.D., M.P.H. – former OHSU Professor and Portland VA physician
  • Dolores Judkins, M.L.S., A.H.I.P. – OHSU Library Associate Professor Emerita
  • Thomas Hacker, M.Arch. – BICC Architect
  • J. Robert (Bob) Beck, M.D. – inaugural Director of the BICC
  • Lesley Hallick, Ph.D. – former OHSU Provost

A lunchtime session featured posters of current projects from BICC entities, including:

  • Library
  • Department of Medical Informatics and Clinical Epidemiology (DMICE)
  • Educational Communications (EdCOMM)

BICC anniversary, celebration, eventA display of computers from the time the building opened, including early Macintosh computers and a NeXT machine that was similar to the one that served as the first Web server, provided a visual representation of how far information technology has come.

The BICC: today and tomorrow

The afternoon session started with short presentations about present programs in the BICC, including an overview of Library activities by Shaffer and an overview of DMICE by Dr. Hersh. Dr. Hersh noted the tremendous return on investment not only in terms of research grants funded but also in contributions to dissemination via educational programs.

Dr. Brennan rounded out the day by charting the future course for NLM library operations, biomedical informatics, data science research, and the future of open science and open data, leaving plenty of time for the audience to provide feedback on her vision and plans. The day ended on a festive note with a reception and open house for the whole campus to celebrate the history and accomplishments embodied in the BICC.

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Do you have questions about data or software sharing?



On Friday, November 4, Technology Transfer & Business Development and the Data Jamboree are co-hosting a panel presentation and round-table discussion on sharing and securing data and software through open source and creative commons licensing.  OHSU community members will learn about the importance of securing rights, as well the ways in which data and software can be licensed to meet researcher and community goals.

Panelists include:

  • Tammy Buist, VP and Chief Business Development Officer, Seattle’s Cancer Research & Biostatistics Institute
  • Brad Biddle, Owner, Biddle Law LLP
  • Frank Curci, Partner, Ater Wynne LLP

The presentations will be followed by two round-table discussions led by OHSU researchers Drs. Kemal Sonmez, Melissa Haendel, and Steven Bedrick.  The round tables will explore goals and issues related to intellectual property, research aims, and scientific communication through the lens of project case studies.  Attendees will have an opportunity to ask questions and share their ideas about what it means and how to share data and software openly and responsibly.

All OHSU faculty, students, and staff are welcome!  Food and drink will be served.

Friday, November 4, 2:00 – 5:00 PM

  • Presentations 2:00 – 3:30
  • Food and drink will be served at 3:30
  • Round table discussions 4:00 – 5:00

Doernbecher Children’s Hospital, Vey Auditorium, 11th floor


This special event is presented by OHSU Technology Transfer & Business Development, Computational Biology, and the OHSU Library.

OHSU Library Collaborates with DMICE to Make Biomedical Big Data Science Open Educational Resources Available

For the last couple years, faculty from the OHSU Department of Medical Informatics & Clinical Epidemiology (DMICE) and Library have been developing open educational resources (OERs) in the area of Biomedical Big Data Science. Funded by a grant from the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) Program, OERs have been produced that can be downloaded, used, and repurposed for a variety of educational audiences by both learners and educators.

Development of the OERs is an ongoing process, but we have reached the point where a critical mass of the content is being made available for use and to obtain feedback. The OERs are intended to be flexible and customizable and we encourage others to use or repurpose these materials for training, workshops and professional development or for dissemination to instructors in various fields. They can be used as “out of the box” courses for students, or as materials for educators to use in courses, training programs, and other learning activities. We ultimately aim to create 32 modules on the following topics:

  1. Biomedical Big Data Science
  2. Introduction to Big Data in Biology and Medicine
  3. Ethical Issues in Use of Big Data
  4. Clinical Standards Related to Big Data
  5. Basic Research Data Standards
  6. Public Health and Big Data
  7. Team Science
  8. Secondary Use (Reuse) of Clinical Data
  9. Publication and Peer Review
  10. Information Retrieval
  11. Version Control and Identifiers
  12. Data Annotation and Curation
  13. Data Tools and Landscape
  14. Ontologies 101
  15. Data Metadata and Provenance
  16. Semantic Data Interoperability
  17. Choice of Algorithms and Algorithm Dynamics
  18. Visualization and Interpretation
  19. Replication, Validation and the Spectrum of Reproducibility
  20. Regulatory Issues in Big Data for Genomics and Health Semantic Web Data
  21. Hosting Data Dissemination and Data Stewardship Workshops
  22. Guidelines for Reporting, Publications, and Data Sharing
  23. Terminology of Biomedical, Clinical, and Translational Research
  24. Computing Concepts for Big Data
  25. Data Modeling
  26. Semantic Web Data
  27. Context-based Selection of Data
  28. Translating the Question
  29. Implications of Provenance and Pre-processing
  30. Data Tells a Story
  31. Statistical Significance, P-hacking and Multiple-testing
  32. Displaying Confidence and Uncertainty

At the present time, 20 of the above modules are available for download and use. We are encouraging their use and seeking feedback from those who make use of them. The feedback will be used to improve the available modules and guide development of those not yet released.

We have also been developing mappings to research competencies in other areas, such as for the NIH Clinical and Translational Science Award (CTSA) consortium research competency requirements and the Medical Library Association professional competencies for health sciences librarians. To this end, we have been able to link these materials to existing efforts, and provide training opportunities for learners and educators working in these areas. We ultimately aim to complete this mapping across all of the BD2K training offerings, to align with other groups, avoid redundancy and to ensure we are meeting the needs of these various groups.

This project is actually one of several projects that have been funded by grants to develop and provide education in biomedical informatics and data science. The other projects include:

We hope that all of these materials are useful for many audiences and look forward to feedback enabling their improvement.

For more information, please contact Nicole Vasilevsky.

Maija Anderson appointed to Associate Professor in the OHSU Library

maijaWe are pleased to announce that Maija Anderson, MA, MLIS was appointed as Associate Professor at OHSU Library. As Director of Curatorial Services, Maija oversees the library’s special collections, university archives, and digital assets management program. Since November 2010, Maija has developed projects and partnerships that bring OHSU history to new audiences, while expanding and improving core services to the university community. Maija has presented and published scholarship on archives management, digitization, and Pacific Northwest medical history, and is an active leader in the Society of American Archivists.

Steve Duckworth, University Archivist

duckworth_2016-10-18-copySteve Duckworth recently joined OHSU Library’s Historical Collections & Archives as the University Archivist. Steve comes most recently from working as the Processing Archivist for the University of Florida. Previously, he served as a Project Archivist for the National Park Service in Anchorage, AK and as an Archives Processor with the “Hidden Collections” project of the Philadelphia Area Consortium of Special Collections Libraries (PACSCL). He has also conducted archival processing in Philadelphia’s John J. Wilcox, Jr. LGBT Archive and the Sigma Sound Studio Audio Archive (at Drexel University), and even once served as the Assistant Librarian for the Allentown (PA) Symphony Orchestra.

Steve has an MSLIS with a concentration in Archives Management from Drexel University (as well as a couple of other degrees in music performance). He has recently completed the Digital Archives Specialist certification from the Society of American Archivists (SAA). He serves on SAA’s Diversity Committee and as a member of the SAA Issues & Advocacy Roundtable’s On-Call Research Teams. He has recently conducted research into artifact processing within traditionally paper-based archival environments and has previously participated with teams that published or presented on web archiving, reprocessing archival collections, and enhancing finding aids for accessibility and usability.

Steve is excited to bring his experience and inquisitive nature to this position where he hopes to enhance current collections while increasing the diversity and substance of the holdings of HC&A. Additionally, he hopes to contribute to a more diverse work place and profession through various initiatives and outreach efforts. Being new to Portland, Steve is also looking forward to exploring this beautiful area and getting to know the people and places that make the Pacific Northwest so unique.


Nicole Vasilevsky appointed to Research Assistant Professor in the OHSU Library




The OHSU Library is pleased to announce that Nicole Vasilevsky, PhD, was appointed to Research Assistant Professor in the OHSU Library. Nicole works as a biocurator and ontologist in the Ontology Development Group. Currently she is focusing on biocuration of the rare disease literature for the Monarch Initiative (, ontology development for the Monarch Disease Ontology, Human Phenotype Ontology and the Cell Ontology, and is developing educational resources for the Big Data to Knowledge projects in DMICE and the Library.

Register for Science Hack Day

Science Hack Day Portland is just a couple days away. Starting with a kick-off reception this Friday at 6:30 PM, OHSU students, scientists, and staff will team up with developers, designers, librarians, roboticists, and science enthusiasts to tackle projects and build new connections.

Science Hack Day Portland is open to everyone, free, and a great opportunity to solve research issues, build your network, and have fun with science! Over 125 attendees have already formed teams to automate lab procedures, visualize and open up data, explore new techniques, and just have fun code and hardware. Want some inspiration? Read about what the OHSU Laboratory of Brain, Hearing, and Behavior will be working on.

You can register for Science Hack Day Portland now, or just show up! You can come with an idea ready to form a team, or just some curiosity and a desire to tinker. Doors open this Friday, October 7, at 6:30 PM at the XOXO Outpost. Food and drink will be provided. No worries if you can’t make it on Friday, you can still join and form teams on Saturday. View the full schedule here.

If you have questions or ideas about Science Hack Day Portland, please contact Robin Champieux at or the event organizers at

OHSU Science Hack Day team aims to reduce human errors with robotic upgrade

shd2In the Oregon Hearing Research Center’s Laboratory of Brain, Hearing, and Behavior, led by Dr. Stephen David, we study how the auditory brain interprets sounds in different behavioral conditions.

Listening to a friend talking in a noisy room seems like an effortless task for most people, but it can be challenging for people with even mild hearing impairments. Understanding how the healthy brain solves these problems is important to develop better treatments for the hearing impaired.

We use a number of techniques to study brain activity during auditory behavior. Recently, we have begun using optogenetics to precisely control neural activity in specific brain regions, which requires shining a laser light over the area under study.

One of the key pieces of equipment for our experiments is a stereotactic micromanipulator. This manipulator has three axes that can be moved to precise, targeted positions by the careful adjustment of manipulator knobs by the skilled hands of one of our lab members. This technique is subject to human error due to relatively low accuracy and replicability of human movements.

In an effort to reduce these potentially confounding human errors, our lab will team up at the first Science Hack Day in Portland (October 7-8) to upgrade our existing manual stereotactic micromanipulator to a robotic one.

We will use affordable, commercially available CNC equipment and open source CNC controlling software such that the experimenter will be able to control the position and the speed of each movement digitally, with a precision of about 3 micrometers per turn. This will make our experimental control about 10 times more accurate and reproducible.