Do not let Excel to deplete your gene list

24 November 2015 - 3:25pm -- Rolando Garcia-Milian

Last night, while preparing an RNAseq dataset for functional analysis. I found this problem again. When opening high-throughput data results into Excel be aware that this software will convert (by default) some gene symbols into a date format- see examples in the table below. These conversions are not reversible so the original name cannot be recovered. Zeeberg et al. reported this problem back in 2004. If you are not aware of this and proceed with the functional analysis, those genes (converted into dates) will not be recognized and will not be computed. If you think that this will never happen to you, this error have been found in a project as important as the Cancer Genome Atlas.  

One way to avoid this –from the end-user bioinformatics perspective- is to define the column containing the gene symbols as “Text” under the “Column data format” as shown in the figure below. It is always recommended –whenever possible- to use unique identifiers (Ensembl IDs, Gene IDs, Affymetrix IDs, etc.) other than gene symbols. If you are not sure, you can always go to the Gene database (NCBI, NIH) whenever looking for the official symbol of a gene.   

For questions, consultations, or help with you functional analysis, please do not hesitate to contact me.

Example of some human gene symbols that will be converted into dates by Excel.

GIDEON: Global Infectious Diseases & Epidemiology Network

18 November 2015 - 4:56pm -- Mark Gentry

GIDEON (Global Infectious Diseases and Epidemiology Online Network) is a global infectious disease knowledge management tool. It is designed to assist in diagnosing infectious diseases and staying current on the latest trends in epidemiology and treatment.  It also provides information on the history of outbreaks.  Gideon is used for diagnosis and reference in the field of tropical and infectious diseases, epidemiology, microbiology and antimicrobial chemotherapy. There is detailed information on vaccines and vaccination throughout the world and an extensive section on worldwide travel.  Access GIDEON at

Great American Smokeout: Key Info Resources

18 November 2015 - 12:27pm -- Andy Hickner

Thursday, November 19 is the American Cancer Society's annual "Great American Smokeout," encouraging smokers to quit, even if it's only for one day.  What better time than to round up a few key information resources on tobacco cessation?

The DynaMed chapter offers patient education materials, as does ClinicalKey.  Click the dropdown menu to the left of the search box to filter results in the "Patient Education" source type. 

Clinical Key smoking cessation

For help finding more evidence on tobacco and smoking cessation, you can always contact your department's librarian


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

5 November 2015 - 9:50am -- 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 -- 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 -- hg48

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 -- 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.


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