Ontology Development Group Announces First Release of Monarch Initiative

Dr. Melissa Haendel and the Ontology Development Group announce the first (sneak peak) release of the Monarch Initiative (http://monarchinitiative.org/). The Monarch Initiative Discovery System will contain a wealth of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors with semantic similarity calculations that suggest novel relationships based on the information content of data descriptions.

Why are we calling this a Sneak Peek? Because we plan to incrementally add functionality over the next few months based on user feedback.The Sneak Peek currently includes phenotype-genotype data from human, mouse, and zebrafish. The system allows comparison of phenotypic profiles (either a disease related set or a user-defined set) across organisms using a semantic similarity algorithm (the OWLsim algorithm) and a suite of integrated phenotype, anatomy, and disease ontologies. Functionality includes the ability to explore the relationships between models, diseases, genes, and phenotypes, including a visualization tool to review phenotypes across models to investigate the degree to which they recapitulate a disease.

Services include an API to retrieve the models most related to any given set of phenotypes, as well as an API call to determine the sufficiency of a phenotype annotation profile. These services are being used within PhenoTips and by the NIH Undiagnosed Disease Program to compare human undiagnosed disease phenotype profiles against model systems to ensure adequate annotation to aid prioritization of gene candidates.

User feedback is welcome, please contact: info@monarchinitiative.org or Melissa Haendel: haendel@ohsu.edu

New Library Books with OHSU Authors, April 2014

Clinical emergency medicine / [edited] by Scott Sherman, Joseph Weber, Michael Schindlbeck, Rahul Patwari.              

Contributors Nicole M. Deiorio and William Thomas Smith affiliated with Oregon Health & Science University.

Clinical manual of contact lenses / [edited by] Edward S. Bennett, Vinita Allee Henry. 

Contributors Eric Kawulok and Derek J. Louie affiliated with Oregon Health & Science University.

Clinical review of oral and maxillofacial surgery : a case-based approach / [edited by] Shahrokh C. Bagheri.      

Contributors R. Bryan Bell, Samuel Bobek, Tuan G. Bui, Eric Dierks, Brett A. Ueeck and David Verschueren affiliated with Oregon Health & Science University.

Core procedures in plastic surgery / Peter C. Neligan, Donald W. Buck II.             

Contributor Mark Laurence Jewell affiliated with Oregon Health & Science University.

Current surgical therapy.            

Contributors Phong T. Dargon, Karen Deveney, Gregory J. Landry, Kresimira Milas, Erica L. Mitchell, K. Shad Pharaon, Lee L. Swanstrom and Donald D. Trunkey affiliated with Oregon Health & Science University.

Ham’s primary care geriatrics : a case-based approach / [edited by] Richard J. Ham, Philip D. Sloane, Gregg A. Warshaw, Jane F. Potter, Ellen Flaherty.   

Contributors Heidi D. Nelson and E. Foy White-Chu affiliated with Oregon Health & Science University.

Immunological mechanisms and therapies in brain injuries and stroke / Jun Chen, Xiaoming Hu, Mary Stenzel-Poore, John H. Zhang, editors.           

Editor and contributor Mary P. Stenzel-Poore and contributors Frances Rena Bahjat, Raffaella Gesuete and Halina Offner affiliated with Oregon Health & Science University.

Medical insurance : an integrated claims process approach / Joanne D. Valerius … [et al.].         

Author Joanne D. Valerius affiliated with Oregon Health & Science University.

Mosby’s review questions for the national board dental hygiene examination / edited and contributed by Barbara L. Bennett.             

Contributor Phyllis L. Beemsterboer affiliated with Oregon Health & Science University.

Occupational therapy for physical dysfunction / editors, Mary Vining Radomski, Catherine A. Trombly Latham.               

Contributors Lois F. Copperman and Lucinda L. Hugos affiliated with Oregon Health & Science University.

Ophthalmology / lead editors, Myron Yanoff, Jay S. Duker   section editors, James J. Augsburger and [11 others].           

Contributor Mark Packer affiliated with Oregon Health & Science University.

Pediatric audiology : diagnosis, technology, and management / [edited by] Jane R. Madell, Carol Flexer.           

Contributor M. Patrick Feeney affiliated with Oregon Health & Science University.

Strauss and Mayer’s emergency department management / by Robert W. Strauss, Thom A. Mayer.        

Contributor Patrick H. Brunett affiliated with Oregon Health & Science University.

OHSU Library and OHSU WRITEs is proud to announce the results of the 2014 Poetry Contest!

Thank you for your submissions! Participating OHSU students, faculty, and staff were creative and inspired us by sharing their experiences so thoughtfully.

We hope you enjoy reading the outstanding poems that were selected for this year’s Poetry Contest.

And the winner is…

More than Cells by Rebecca L. Smith

Honorable mentions include:

Artist, Turned Physician by Kate Marshall

First Year A Gap by Julia Armendariz

ProQuest PsycARTICLES and PsycINFO on trial

The PsycARTICLES database offers full-text articles for journals published by the American Psychological Association, the APA Educational Publishing Foundation, the Canadian Psychological Association and Hogrefe & Huber. The database includes all material from the print journals. Many titles go back to volume 1, issue 1.

The PsycINFO database is published by the American Psychological Associations and provides comprehensive indexing and abstracts of the international psychological literature from the 1800s to the present. Documents indexed include journals, articles, books, dissertations and more. 90% of the 3,000+ titles indexed in PsycINFO are peer-reviewed.

PsycARTICLES Trial Access

PsycINFO Trial Access

Once you have explored PsycARTICLES and/or PsycINFO please help us to inform our purchase decision by completing the very brief survey(s) at:

This trial is open until April 18th, 2014.

Questions? Contact:

Tami Wilkerson wilkerst@ohsu.edu 503-494-0690

New Library Books with OHSU Authors, February 2014

Abrams’ angiography : interventional radiology / editors, Jean-Francois H. Geschwind, Michael D. Dake.

Contributors Jessica H. Duman, Khashayar Farsad, John A. Kaufman, Frederick S. Keller, Kenneth J. Kolbeck and Josef Rosch affiliated with Oregon Health & Science University.


Case studies in pediatric emergency and critical care ultrasound / edited by David J. McLario, John L. Kendall.

Contributor Catherine Erickson affiliated with Oregon Health & Science University.


Computational systems biology : from molecular mechanisms to disease / edited by Roland Eils, Andres Kriete.

Contributor Paul Spellman affiliated with Oregon Health & Science University.


Curbside consultation in cataract surgery : 49 clinical questions / edited by Terry Kim.

Contributor Richard S. Hoffman affiliated with Oregon Health & Science University.


Diagnostic imaging. Emergency / [edited by] R. Brooke Jeffrey… [et al.].

Contributors Bronwyn E. Hamilton, Gary M. Nesbit and Roya Sohaey affiliated with Oregon Health & Science University.


Diagnostic pathology. Transplant pathology / [edited by] Anthony Chang.

Contributor Joseph Ahn affiliated with Oregon Health & Science University.


Emergency medicine procedures / [edited by] Eric F. Reichman.

Contributor O. John Ma affiliated with Oregon Health & Science University.


Ma and Mateer’s emergency ultrasound / [editors] O. John Ma … [et al.].

Editor O. John Ma affiliated with Oregon Health & Science University.


Mastery of endoscopic and laparoscopic surgery / edited by Lee L. Swanstrom… [et al.].

Contributors John G. Hunter, Renato A. Luna, Lee L. Swanstrom, Corey E. Van Hove and Mark Whiteford affiliated with Oregon Health & Science University.


Modern community mental health : an interdisciplinary approach / [edited by] Kenneth R. Yeager…[et al.].

Contributors Bentson McFarland, David A. Pollack, Craigan T. Usher and Vikki L. Vandiver affiliated with Oregon Health & Science University.


Neuropsychological aspects of substance use disorders : evidence-based perspectives / edited by Daniel Allen and Steven Paul Woods.

Contributors Marilyn Huckans, Amanda M. Barkley-Levenson and Jennifer M. Loftis affiliated with Oregon Health & Science University.


Osteogenesis imperfecta : a translational approach to brittle bone disease / editor Jay R. Shapiro.

Contributors Elizabeth Martin and Eric S. Orwoll affiliated with Oregon Health & Science University.


Strauss and Mayer’s emergency department management / chief editors Robert W. Strauss, Thom A. Mayer.

Contributor Patrick H. Brunett affiliated with Oregon Health & Science University.


Wintrobe’s clinical hematology / editors, John P. Greer…[et al.].

Contributors David C. Calverley, Suman Malempati and H. Stacy Nicholson affiliated with Oregon Health & Science University.

PsycTESTS now available through the OHSU Library

The OHSU Library is now providing access to the PscyTESTS database.

Updated monthly, this repository for ready-to-use tests and measures from the APA features instruments that are relevant to psychology and related fields, such as psychiatry, education, medicine, business, social work and more.

International in scope, this resource provides access to thousands of actual test instruments, most of which are available for immediate download and use in teaching and research. PsycTESTS is an authoritative source of structured information about tests of interest to a variety of fields, and while focused on contemporary instances of test use, has coverage that spans more than a century.

Each detailed test record includes a summary, background information, development history, purpose, reliability and validity data (when available), test format and the citation for the peer-reviewed source document.

Help make basic science more reproducible and get free stuff

The issue of scientific reproducibility has been at the forefront of the news recently, from the Economist highlighting the lack of reliable research in “Trouble at the Lab” to Francis Collin’s recent Nature article describing the NIH’s new policies to improve reproducibility.  Recently, Dr. Haendel’s group in the Library published a paper (Vasilevsky et al, 2013, PeerJ) showing that a key component of scientific reproducibility, the ability to identify the research resources used in a study, is problematic.

To address this issue, the Resource Identification Initiative is developing a process and tools to make it easier to identify research resources used in the materials and methods of biomedical research through the use of unique identifiers. Numerous publishers, including PLoS, Elsevier and Wiley, as well as editors, and the NIH have come together to pilot a program where authors aid in the specific identification of resources prior to publication.

The Resource Identification Initiative is seeking beta tester authors and endorsers.  Participants will receive prizes.  To become a beta tester, please go here: http://www.antibodies-online.com/resource-identification-initiative/

For more information, please contact:

Food for Fines

Library Closure-Monday, February 17th, 2014

The OHSU Library will be closed Monday, February 17th, 2014 in observance of Presidents’ Day.

The After Hours Study Space will be available for OHSU students, faculty and staff. Remember your ID!

The library will resume regular hours on Tuesday, February 18th, 2014.

For additional information on library hours see http://www.ohsu.edu/xd/education/library/about/hours.cfm.

Books 24×7 Service Cancellation

Due to budget constraints the library has made the difficult decision to cancel Books 24×7. We apologize for the loss of this resource.  Our decision was based on the cost of the resource and its overall low usage. We recognize that several Books 24×7 titles were well used and we are looking into other options for access.  If you would like us to consider purchasing one or more of the Books 24×7 titles, please let us know via our Suggest Purchase form.  You only need to include the title and your contact information.

Additionally, the Springer EBooks collection includes many business, management and information technology titles including Lecture Notes in Computer Science.

If you have any questions or concerns please contact libacq@ohsu.edu.