Trial for new apps: EBM Guidelines, DSM 5 Differential Diagnosis

5 November 2015 - 9:50am by Andy Hickner

Unbound Medicine

The Cushing/Whitney Medical Library is trying out two new Unbound Medicine apps through the end of November: "Evidence Based Medicine Guidelines" and the "DSM 5 Differential Diagnosis Handbook." To get these apps on to your device, make sure that you have the Unbound Medicine app installed and accept any update notifications that you're presented with. For information about downloading the Unbound Medicine app to your device, please see the Medical Library's "Mobile Device Applications" page at

The Bamberg Surgery: An early European surgical text

3 November 2015 - 10:51am by Andy Hickner

Bamberg Surgery

Monica Green, a scholar of the history of medieval medicine, recently profiled the Bamberg Surgery, which is part of the Medical Historical Library's collection.  The Bamberg Surgery is a surgical text dating from the mid-12th century which was acquired by Dr. Harvey Cushing and subsequently formed part of the original Medical Historical collection at Yale. 

Green writes:

The Bamberg Surgery doesn’t get a lot of love in histories of surgery, because of its patchwork character. As Corner himself said, “it is a notebook, a partially organized collection of notes, memoranda, prescriptions, and excerpts from other books.” But the Bamberg Surgery merits a closer look to contemplate the question with which we began: how do you begin to build up a body of written surgical knowledge when previously you had none?

The Bamberg Surgery draws selectively from the (now complete) translation of (Persian physician​‘Ali ibn al-‘Abbas) al-Majusi’s text, which it fuses with an early medieval text on phlebotomy that circulated under Hippocrates’ name. It then expands on these elements with new pharmaceuticals, new techniques, and elements of anatomical and physiological learning drawn from other texts. For example, al-Majusi’s text had never mentioned marciaton, a compound medicine for a wax-based unguent passed on through the early medieval Latin pharmaceutical tradition. The Chirurgia salernitana had recommended its use, and we find it in the Bamberg Surgery likewise, being recommended for nerve damage from a wound, broken bones, and dislocations.

Similarly, the author cites Galen’s Tegni several times, a translation of the foundational handbook of medicine composed by the 2nd-century Greek polymath, used widely in the Islamic world and, increasingly, in Europe as a basic introduction to medical theory and practice.

Bamberg Surgery

Click here to read Green's full post, which discusses a number of other medieval surgical texts. 


The Yale MeSH Analyzer

2 November 2015 - 1:28pm by Holly Grossetta Nardini

Yale MeSH Analyzer

The Yale MeSH Analyzer

Two of our librarians, Lei Wang and Holly Grossetta Nardini, have developed a web-based tool to simplify search design and refinement for major, comprehensive database searches. This tool was released at NAHSL’15 in Providence this past October and is primarily for those involved in comprehensive database searching and systematic review research teams.

At Yale, based on work by Jan Glover, we have a "best practice" for major searches: creating a MeSH analysis grid. A MeSH analysis grid helps us identify problems in a search strategy by showing how key articles are indexed in the MEDLINE database in an easy-to-scan tabular format. Creating a MeSH analysis grid manually is useful for search validation but time-consuming.

The Yale MeSH Analyzer removes the tediousness from the process by automatically retrieving the article metadata and formatting and generating a grid. Using the tool is easy: simply paste a list of up to 20 PMIDs into the text box and click "Go.” You can delimit the PMIDs in any way you like, even pasting in a paragraph that includes text. The Analyzer will scan for PMIDs and attempt to retrieve article data from PubMed, creating a grid in either HTML or Excel for you to manipulate. There are other customizable options, and you can install a browser button on your toolbar to do an analysis in one step.

You can then easily scan the grid and identify appropriate MesH terms, term variants, indexing consistency, and the reasons why some articles are retrieved and others are not, a common frustration for expert searchers. This inevitably leads to fresh iterations of the search strategy to include new terms. In addition to MeSH terms, author-assigned keywords, article titles, and abstracts can be included in the analysis display. 

We hope that this tool helps you refine your searches and saves you time. We would love to hear your feedback.

Interlibrary loan is back up (update)

29 October 2015 - 4:11pm by Andy Hickner

Update:  As of Thursday night, ILLiad is back up and running.  Thanks for your patience.

ILLiad, the library's interlibrary loan system, is not functioning. Library ITS is working on a solution to fix this issue as soon as possible. This means we are currently unable to order any materials for users, nor can users submit requests. Please check back for updates.

Get your omics functional analysis done: upcoming trainings on Ingenuity Pathway Analysis and MetaCore

15 October 2015 - 4:45pm by Rolando Garcia-Milian

The Yale Medical Library is providing to all Yale affiliates free access to two of the most powerful commercial bioinformatics tools for the analysis of omics data: MetaCore and Ingenuity Pathway Analysis. This is part of a pilot project conducted by the medical library in order to find sustainable and long term access to these tools. Please register for these upcoming trainings if you are interested in learning how to use these tools or if you need a refresher.

For questions on how to register for an account or comments please contact Rolando Milian

Title: Introduction to Ingenuity Pathway Analysis


  • What is IPA and what questions can it address?
  • Overview of key features in IPA
  • Ingenuity Knowledge Base
  • Search & Pathway Building - Gene/ Chemical, Functions, Drug Targets
  • Advanced Search: Limiting results to a molecule type, family or disease-association.
  • Building pathways: Creating a pathway, pathway navigating, Using Build and Overlay tools
  • Bioprofiler
  • Dataset Analysis: Interpretation of Gene, Transcript, Protein and Metabolite Data
  • Data Upload and Analysis:  Uploading and formatting a dataset, setting analysis parameters and running an analysis
  • Pathway Analysis and Canonical Pathways
  • Downstream Effects Analysis and identifying downstream functions and processes that are likely affected
  • Upstream regulators Analysis
  • Causal Network Analysis and identifying likely root regulators
  • Regulator Effects Analysis to link upstream regulators with downstream functions and processes that are affected
  • Comparison analysis and comparing multiple observations

Date & Time:      9:00am - 12:00pm, Tuesday, October 27, 2015

Location:              H-203, Jane Ellen Hope Building, 315 Cedar St, New Haven CT

Presenter:          Field Scientist QIAGEN Informatics

Register here     


Title:      MetaCore: Getting the most from your "omics" analysis (Introductory session)

Description: The ability to generate massive amounts of data with "omics" analysis begs the need for a tool to analyze and prioritize the biological relevance of this information. GeneGo provides a solution for using "omics" gene lists to generate and prioritize hypotheses with MetaCore. This tutorial highlights how to work with different types of data (genomics, proteomics, metabolomics and interaction data) beginning with how to upload gene lists and expression data (if available). Here we demonstrate data manager capabilities including how to upload, batch upload, store, share and check data properties and signal distribution. We then focus on how MetaCore uses your gene list to extract functional relevance by determining the most enriched processes across several ontologies. This entails a detailed lesson on how to prioritize your hypothesis using the statistically significance enrichment histograms and associate highly interactive GeneGo Maps and pre-built networks. We further emphasize the role of expression data in your analysis and the ability to visually predict experimental results, associated disease and possible drug targets. Lastly we highlight the benefits of using MetaCore workflows to compare data sets and work with experiment intersections.

Date & Time:      10:00am - 12:00pm, Tuesday, November 3, 2015

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters

Register here      

Title:      MetaCore: Getting the most from your "omics" analysis (Advanced)

Description: In the advanced tutorial, we will explore uses of our network building algorithms and methods for hypothesizing key hubs passed on data. We will begin this session with a discussion on using the Key Pathway Advisor to hypothesize key hubs regulating gene expression data. The session will then review ways of using the 11 network building algorithms in MetaCore. The first example will review how to build a network purely from the curated knowledge within MetaCore. Then we will go through an example of using omics data to build a network of interactions to better understand the relationships within our data.

Date & Time:      1:00pm - 3:00pm, Tuesday, November 3, 2015

Location:              C-103 - SHM 333 Cedar St, New Haven CT 06520

Presenter:          Dr. Matthew Wampole, Solution Scientist, IP & Science, Thomson Reuters

Register here     


Join the End-user Bioinformatics Group and become a member of a community that collaborates on end-user bioinformatics events, training sessions, resources, and tools that support biomedical research at Yale.

Open Access Week, October 19-25

13 October 2015 - 4:10pm by Andy Hickner

From October 19-25, the Yale Library is celebrating international Open Access Week with a series of wide-ranging events.  Events will focus on topics from the use of data, images and government documents, to knowing your rights as an author and understanding "predatory publishers."

What is Open Access Week?  Here's a taste, from the week's official website: 

Open Access Week, a global event now entering its eighth year, is an opportunity for the academic and research community to continue to learn about the potential benefits of Open Access, to share what they’ve learned with colleagues, and to help inspire wider participation in helping to make Open Access a new norm in scholarship and research.

“Open Access” to information – the free, immediate, online access to the results of scholarly research, and the right to use and re-use those results as you need – has the power to transform the way research and scientific inquiry are conducted. It has direct and widespread implications for academia, medicine, science, industry, and for society as a whole.

All events are listed on the library calendar.

Picturing Medical History: the Hansen gift

5 October 2015 - 4:03pm by Andy Hickner

Bert Hansen(Post authored by Melissa Grafe)

The Medical Historical Library announces a new gift encompassing visual materials depicting medical practice, public health, disease, and more from the collection of Bert Hansen, Ph.D.

Over a period of thirty years, Bert Hansen actively collected original materials to document and exhibit the visual record of public health and medical practice and research in America, primarily in graphics published in popular media.  Hansen has been teaching history at Baruch College of CUNY since 1994. He holds degrees in chemistry (Columbia) and history of science (Princeton).  Prof. Hansen has written on obstetrics teaching in the 1860s, the new medical categorization of homosexuals in the 1890s, the advocacy for public health and sanitation in political cartoons from 1860 to 1900, and the popularity of medical history heroes in children’s comic books.  His book, Picturing Medical Progress from Pasteur to Polio: A History of Mass Media Images and Popular Attitudes in America (Rutgers University Press, 2009), was honored with an award from the Popular Culture Association and named to the “2010 Best of the Best” for Public and Secondary School Libraries by the American Library Association.

Recently, Hansen began transferring his collection to the Medical Historical Library.  The library was given over 600 prints, including chromolithographs and wood engravings from 19th-century magazines like Harper’s Weekly, Frank Leslie’s, Puck, and Judge.  Hansen also donated 20th-century popular magazines such as Life and Time, which reported on medical issues.  LIFE magazine published serious photographic essays about medical subjects on a regular basis, at least 1100 of them in its 1900 weekly issues.  Because few libraries have preserved this magazine, Hansen collected several hundred issues with medical stories to document the way the mid-20th century public was taken into operating room, the laboratory, and the mental asylum.

For Hansen, the central research question animating the collection was:  Just what did medicine look like to the average person (not to the insiders within the profession)?  All the images were collected to answer that question.  In addition to news sketches in magazines like Harper’s Weekly, political cartoons turned out to be a remarkable source of visual evidence.  Medicine itself was rarely the object of the caricature, but when a president is shown as a doctor looking through a microscope or amputating a limb, or portrayed as a midwife with forceps or a nurse tending to a patient in bed, we get a sense of stereotypes and popular expectations.  Despite comic exaggerations, these images had to be sufficiently true-to-life for the political message to be understood.

Life magazine from Hansen collectionHansen has also donated a small collection of manuscripts, which includes diaries, notebooks, casebooks, and scrapbooks by medical practitioners or on medical themes.  Future parts of the gift will include hundreds of examples of ephemera, from agencies such as health departments and corporations like Met Life, all of which used graphics to convey their messages to the public.  There will also be publicity materials for radio broadcasts and Hollywood films about physicians.  The collection also includes about two dozen highly illustrated juvenile biographies of physicians, and over 100 medically themed comic books.  In addition to the unique original materials, Hansen’s collection contains about ninety 3-ring binders containing photocopies of relevant images (both those in the collection and others that are not).  All the items in the binders and in the collection of originals are recorded in a database with over 4500 entries, which can be searched by keyword, publication, genre, medium, artist, date, etc., and will be made available at a future date.

For questions concerning the collection, please contact Melissa Grafe, Ph.D, John R. Bumstead Librarian for Medical History:

Subscribe to RSS - blogs