Martin Luther King Jr. Holiday Hours

OHSU Library at the BICC  

The Library Service Desk at the BICC will be closed and the Library is not open to the general public on Monday, January 16th, in recognition of the Martin Luther King Jr. holiday.

The After Hours Study Space is open on the 4th floor of the BICC. It may be accessed through the 4th floor entrance with a valid OHSU badge.

Graduate LRC at the CLSB

The Library Service Desk at the LRC will be closed on Monday, January 16th, in recognition of the Martin Luther King Jr. holiday.

The Graduate LRC is open on the 5th floor of the CLSB. It may be accessed with a valid OHSU badge by occupants of departments and programs located at the CLSB.

Vote for OpenTrialsFDA

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Public voting for the Open Science Prize closes this Friday, January 6, and OpenTrialsFDA, led by OHSU Associate Professor, Dr. Erick Turner, is one of the finalists.  This week the OHSU community is rallying to get OpenTrialsFDA shortlisted to receive the $230,000 prize.  The Open Science Prize is a partnership between the NIH, the Wellcome Trust, and the Howard Hughes Medical Institute to “unleash the power of open content and data to advance biomedical research” and its application to improve health.  OpenTrialsFDA is one of six international teams that have been working since May 2016 to build prototypes that realize this vision.

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While the boundaries of Open Science are debatable, in practice its advocates aim to make scientific research freely accessible and maximally interoperable to drive discovery, economic growth and human health.  Increasingly, the most vocal advocates for open science practices are scientific thought leaders, funders, and policy makers — stakeholders that truly influence how we work.  Indeed, in early December, the NIH Office of the Associate Director for Data Science hosted the Open Data Science Symposium, a public event exploring how Open Data and Open Science are transforming biomedical research.  Nearly 1,200 people attended and listened to both the current and a former NIH director passionately and practically describe the importance of data sharing for accelerating research.

Dialogue on Open Science between NIH Director Dr. Francis Collins and Former NIH Director Dr. Harold Varmus, moderated by Chris Wiggins, Chief Data Scientist for The New York Times. Image: https://datascience.nih.gov/blog/OpenDataScienceSymposium2016

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OpenTrialsFDA is designed to make clinical trial data from FDA reviews more discoverable, searchable, and actionable.  It addresses important problems and has broad clinical relevance.  Unlike the published literature, which often provides a biased picture of drug efficacy and safety, FDA reviews contain comprehensive methodological, protocol, and outcomes information.  While the FDA makes this data available via a public database, the documents are difficult to search and link to other content; therefore, it is underutilized by researchers, clinicians, and the public.  OpenTrialsFDA fixes this problem, and combined with its parent project, OpenTrials,  provides a linked foundation of publically accessible clinical trial data to inform clinical decision making and new research.

OpenTrialsFDA needs your votes to win the Open Science Prize, which will allow Dr. Turner and his team to fully develop this important tool.  Only 3 teams will be shortlisted and considered by the expert panel of advisors for the $230,000.  You can learn more about OpenTrialsFDA via this short video and explore the prototype.

Vote here and spread the word by Friday, January 6 at 11:59 PM PST to make OpenTrialsFDA and OHSU an Open Science Prize winner! 

Additionally, if you’re looking for a deep dive on the Open Science Prize and reflections on how to evaluate the finalists, read this post from OHSU Associate Professor, Dr. Melissa Haendel.

Holiday Hours

OHSU Library at the BICC

Monday Dec 26 CLOSED
Monday Jan 2 CLOSED

The After Hours Study Space is on the 4th floor of the Library. It may be accessed through the 4th floor entrance when the Library is closed with a valid OHSU badge.

Graduate LRC at the CLSB

Monday-Friday Dec 26-Jan 2 CLOSED

Access with OHSU badge 24 hours a day

Join us for a special OHSU Open Science Data Jamboree & Hackathon

blogpostThe December Data Jamboree will focus on the power of open content and data to advance biomedical research and human health.  Dr. Erick Turner, Associate Professor at OHSU and Staff Psychiatrist at the Portland VA Medical Center, will introduce OpenTrialsFDA, which is a finalist for the highly competitive Open Science Prize.

OpenTrialsFDA aims to increase access to and the utility of FDA drug approval packages. These review packages often contain information on clinical trials that have never been published.  When these “inconvenient truths” are integrated into a systematic review or meta-analysis, it can sometimes dramatically shift a drug’s risk-benefit ratio.

Although the FDA makes the reviews available via its web portal Drugs@FDA, the documents are notoriously difficult to search and aggregate. As a consequence, they are rarely used by clinicians and researchers, despite their immense value.  OpenTrialsFDA intends to change this by allowing researchers, clinicians, the public, developers, and third party platforms to access, search, and build upon this data.

Dr. Turner’s keynote talk will be followed by an overview of the NIH’s new clinical trial data sharing requirements and two concurrent hands-on sessions:

  • The first will be a deep dive on searching OpenTrialsFDA website, understanding the contents of an FDA drug approval package (including the statistical content), and how to use the data for different use cases, such as meta analysis and systematic reviews.  Dr. Turner will team teach the breakout with an OHSU biostatistician.
  • The second will be a OpenTrialsFDA hackathon using the OpenTrials API.  Attendees will have the opportunity to use their research, development, clinical, and visualization expertise (to name a few) to explore, present, and build upon the OpenTrials data and the OpenTrialsFDA application.  Please note, no technical expertise is required, as there will be multiple ways of contributing.

The Data Jamboree is presented by Computational Biology and the OHSU Library.  All are welcome to attend, including OHSU faculty, students, and staff as well as Portland area science enthusiasts and developers!

December 16, 2016

2:30 – 5:00 PM (hackathon will continue past 5:00)

Collaborative Life Sciences Building (CLSB), 3A003

Food & Drink provided

Contact:  Robin Champieux, Scholarly Communication Librarian, champieu@ohsu.edu

Holiday Hours

Thursday, November 24, 2016 the OHSU Library service desk at the BICC and the Graduate LRC at the CLSB will be closed in observance of Thanksgiving Day.  The service desk at the Graduate LRC will also be closed on Friday, November 25, 2016.

The After Hours Study Space is on the 4th floor of the Library. It may be accessed through the 4th floor entrance when the Library is closed with a valid OHSU badge. The Graduate LRC is accessible with OHSU badge for departments and programs located at CLSB 24 hours a day.

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.

Original Post:  http://www.ohsu.edu/xd/education/schools/school-of-medicine/news-and-events/bicc-anniv.cfm

Do you have questions about data or software sharing?

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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

Questions:  champieu@ohsu.edu

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.