Librarians at Yale-New Haven Hospital on March 22

16 March 2016 - 5:22pm by Andy Hickner

Medical Librarians will be available on Tuesday, March 22, from 9:30 am- 2:00 pm, on the second floor of Yale-New Haven Hospital, above the atrium, to show you the most recent online information resources including useful mobile apps.  They will also be highlighting a new clinical decision support tool, DynaMed Plus, which is currently located in EPIC and on the clinical work station.  Please stop by to ask questions about what the library can offer you to help support your clinical work, research and education/teaching needs.

One month trial of PsycEXTRA, a grey literature database

16 March 2016 - 9:47am by Andy Hickner

The Library has a one month trial to PsycEXTRA, a grey literature database.

PsycEXTRA, produced by the American Psychological Association, is the premier resource for gray literature relating to behavioral sciences, ethics, health, psychology, and social sciences. It proactively uncovers and presents new developments and research in these disciplines and allows behavioral science researchers to go beyond traditional peer-reviewed materials and locate research before it appears in published journals and books. When combined with conventional research materials, this database allows users to gain vital insight across these disciplines.

Document types in this database include hard to find materials such as amicus briefs; bibliographies; blogs; brochures; clinical trials; conference materials; consumer brochures; curricula; data; directories; dissertations; fact sheets; government reports; grants; guidelines; interviews; legal testimony; legislation; magazines and periodicals; monographs; multimedia; newsletters; newspapers; oral histories; patents; patient-oriented fact sheets and brochures; policy statements; press releases; reports; speeches; standards; technical and annual reports; testimonies; theses; and web articles.

This database includes international materials from countries such as Australia, Canada, Ireland, Latvia, Norway, Sweden, and the United Kingdom, as well as organizations such as academic and research institutions; foundations; the military; national, state and regional psychological associations; federal and state agencies; and international organizations such as the United Nations and World Health Organization.

Updated biweekly, this database includes records for items published from 1825 to the present, none of which overlap with PsycINFO.

Users can browse this database by topic, year, author, document type, or content owner; can search it by content owner, keywords, author names; and publication titles; or can use the Thesaurus of Psychological Index Terms to navigate their way through the database.

We ask users to explore this resource and to send any feedback to your departmental or personal librarian. The trial runs through April 13.

More publishers now requiring ORCID iDs

4 March 2016 - 2:15pm by Andy Hickner

In January 2016, ORCID announced that a number of publishers - eLife, PLOS, the Royal Society, IEEE, AGU, EMBO, and Science - plan to require submitting authors to register for and provide ORCID IDs.  

In its own words,

ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. ORCID is unique in its ability to reach across disciplines, research sectors and national boundaries. It is a hub that connects researchers and research through the embedding of ORCID identifiers in key workflows, such as research profile maintenance, manuscript submissions, grant applications, and patent applications.  

ORCID provides two core functions: (1) a registry to obtain a unique identifier and manage a record of activities, and (2) APIs that support system-to-system communication and authentication.

As ORCID puts it,

Benefits for researchers, in addition to improved discoverability of their works, include single sign-on across journals and streamlined data entry.  The recent launch of Crossref’s auto-update functionality means that researchers can opt to have their ORCID record automatically updated when their papers are published, which in turn means that university and other systems can receive updates directly and reduce reporting burden on researchers.

To learn more about the benefits of ORCID and how to get started, contact your departmental librarian

Transparency and Openness: TOP Guidelines will promote standards in biomedical publishing

3 March 2016 - 9:49am by Andy Hickner

(by Kate Nyhan)

Because the Cushing/Whitney Medical Library supports both students and researchers, we pay special attention to trends in science policy and scholarly communication. One initiative I'm watching and applauding is the Transparency and Openness Promotion Guidelines -- TOP Guidelines for short. Journals, publishers, scholarly societies, and repositories are signing on to these standards to promote transparency and reproducibility. Marcia McNutt, president-elect of the National Academy of Sciences and editor-in-chief of Science discussed this movement at AAAS 2016, and I encourage you to learn more about the project by reading “Promoting an open research culture.”

How will the TOP Guidelines affect researchers at the Yale Schools of Public Health, Medicine, and Nursing? Well, it depends on the journals where researchers hope to publish. Science, PLoS Medicine, and more than five hundred other journals have signed on to the guidelines, and you can check to see if the journals where you plan to publish have also signed on here. But you'll need to get a little more granular, because the TOP Guidelines are actually eight modular standards, each of which can be accepted at four levels.

Science policy goals

Standards from the TOP Guidelines

Reward researchers who engage in open practices through:


  • Citation standards
  • Replication

Support replication and evaluation by describing “transparency” in practical terms:

  • Analytic methods (code) transparency
  • Research materials transparency
  • Design and analysis transparency
  • Data transparency

 Support preregistration through:

  • Preregistration of analysis plans
  • Preregistration of studies

The levels allow journals to find the "sweet spot," as Dr. McNutt put it in her remarks at AAAS: verification, openness, transparency, or mere encouragement. Verification involves ascertaining compliance or validity; openness means that authors must make evidence widely available; transparency means authors state what they have done regarding data sharing, code sharing, and preregistration; encouragement is, well, encouragement, but not a mandate.

I encourage everyone to check out the TOP Guidelines documentation, no matter where you publish. You may decide to hold yourself to some or all of the TOP Guidelines, whether you currently publish in TOP signatory journals or not; you may even decide to start framing student assignments in similar terms. All of us need to keep up with changing expectations in scholarly communication.

I'd love to talk with you, your class, or your journal club about what to expect from funders and journals in the near future. Contact me at

Jeannette Ponzio: 50 Years with the Library

2 March 2016 - 3:14pm by Andy Hickner

(by Katie Hart)

Since she joined the library in 1965, Jeannette Ponzio has witnessed the Cushing/Whitney Medical Library evolve significantly. Interim Director, John Gallagher, sat with Jeannette, the library’s longest serving employee, for a conversation about her many years of exceptional service.

JG:       Jeannette, tell me about when you first joined the Medical Library. What was it like then? What was your first job?

JP:        Before coming to Yale University, I worked as a bookkeeper at the American Supply Company after receiving my bookkeeping certificate from New Haven’s Stone Business College. I began working at Yale in October of 1965. My first job was as a shelver in the Medical Library. Back then books and journals were all that there was, so my days were very busy re-shelving materials in the stacks and helping patrons to find books and articles. The stacks weren’t as large then as they became after the major renovation in the 1990’s. The Circulation Department back then was a part of the Reference Department and the Circulation Desk just off the rotunda where the entrance to the Information Room is now.

John Gallagher & Jeannette Ponzio

John Gallagher & Jeannette Ponzio

JG:       What was your next job?

JP:        In 1971 Stanley Truelson, who was the Director of the Library then, created a part-time evening position for me in Circulation. My husband and I were expecting our first child, and it was important to me to be able to spend the days with her. Times were very different then and Stanley even permitted me to train my husband to do my job while I was out on maternity leave. It worked out great for us. I enjoyed working nights and continued to do so for the next 11 years.

JG:       Over the last 50 years you have seen so many changes. What are some of the most significant ways that the library has changed from your perspective?

JP:        So many things have changed! I don’t know where to begin! The switch from GEAC to Orbis for the library catalog was huge. Also significant was the switch from using photocopy auditrons to copy cards in the ‘80s was another radical change. Finally, now that our users can access so many of the resources they need though our website has really made it easier for them to find the information they need. I can’t imagine what the next major change will be, but the library has always been good at anticipating what our users want. There’s always something fun and new.

JG:       Tell me about your current responsibilities. How did you find yourself in Collection Development and Management?

JP:        After working as the acting head of Circulation in the mid ‘80s, I made the switch from the frontlines of Circulation to supporting back-office operations in 1990, and I have had numerous Technical Services responsibilities since then. Most of my time has been spent on the acquisitions side, helping purchase materials for our patrons and coordinating the work of 3 other people as lead person. Most recently however I have become more involved in the World Health Organization’s HINARI initiative, updating our holdings in the National Library of Medicine’s DOCLINE database, and working with the Access & Delivery Service’s staff to prepare and process print journals and books for transfer to the Library Shelving Facility.

JG:       What has been the best thing about working here for so long?

JP:        Undoubtedly it’s the people. It’s been wonderful over the years to work with so many lovely and dedicated people. With all the changes there’s always someone there to help and train you. It has been great, and a wonderful place to work!

JG:       Thank you Jeannette. On behalf of the Library and Yale we are so grateful for all the wonderful contributions you have made, and for your 50 years of dedicated service! 

On-site NCBI Bioinformatics Workshop at Yale School of Medicine

24 February 2016 - 2:00pm by Rolando Garcia-Milian

On April 5 and 6, Dr. Peter Cooper*** will provide training in the form of four workshops (see below) on the some of the most valuable National Center for Biotechnology Information bioinformatics resources and tools at Yale School of Medicine. This training is hosted by the Yale Cushing/Whitney Medical Library. Although free and open to any Yale affiliate, it is recommended to register since seating is limited.  

Please contact Rolando Milian for questions on these sessions: 203-785-6194


A Practical Guide to NCBI BLAST

Register here

This workshop highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2-Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; IgBLAST, a tool for analysis of antibody and T-cell receptor sequences; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret.

Date:                     Tuesday, April 5, 2016

Time:                     9:00am - 12:00pm

Location:              C-103 - SHM 333 Cedar St, New Haven CT 0652


Accessing Genomes, Assemblies and Annotation Products

Register here

You will learn how NCBI processes genome-level data and produces annotation through the prokaryotic and eukaryotic genome annotation pipelines. You will find, browse, and download genome-level data for your organism of interest and for environmental and organismal metagenomes using the Genome, BioProject and Assembly resources. In addition to assembled and annotated data, you will retrieve and download draft whole genome shotgun and read-level next-gen sequencing data from the Nucleotide and Sequence Read Archive (SRA) databases. You will access results of precomputed analyses of genomes, as well as perform your own analyses of assembled and unassembled genomic data using NCBI's genome BLAST and SRA-BLAST services.

Date:                     Tuesday, April 5, 2016

Time:                     1:30pm - 4:00pm

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


Accessing NCBI Human Variation and Medical Genetics Resources

Register here

You will learn to use and access resources associated with human sequence variations and phenotypes associated with specific human genes and phenotypes. The workshop will emphasize the Gene, MedGen and ClinVar resources to search by gene, phenotype and and variant respectively. You will learn how to map variation from dbSNP and dbVAR onto genes, transcripts, proteins, and genomic regions and how to find genetic tests in GTR. You will also gain experience using additional tools and viewers including PheGenI, a browser for genotype associations and the new Variation Viewer the 1000 Genomes Browser, which provide a useful ways to search for, map and browse variants as well as upload and download data in genomic context.

Date:                     Wednesday, April 6, 2016

Time:                     9:00am - 12:00pm

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


Exploring Gene Expression Information at the NCBI

Register here

You will find, display and analyze microarray and sequence-based expression data that are stored in the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), UniGene, and Epigenomics databases to investigate the potential for expression of transcript splice variants and examine the levels of expression under varied experimental conditions as well as in different tissues and disease states. You will analyze Microarray data the on-demand GEO2R tool and will explore the precomputed transcript analyses that are displayed on the UniGene and GEO Profiles pages. You will explore genome-aligned RNA-Seq data through the Gene database's sequence viewer displays and analyze raw RNA-Seq reads in the SRA database using NCBI's SRA-BLAST service.

Date:                     Wednesday, April 6, 2016

Time:                     1:30pm - 4:00pm

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

***Dr. Peter Cooper, Staff Scientist, National Center for Biotechnology Information (NCBI) directs the scientific outreach and training program for the National Center for Biotechnology Information at the National Library of Medicine. Peter has conducted and developed training courses for biologists in the use of NBCI molecular databases and has provided scientific user support for the NCBI since 1998. Prior to joining the NCBI Peter pursued diverse biological research interests including peptide neurochemistry, marine environmental toxicology, and taught biology and chemistry. Peter earned a BS from Virginia Tech, a MA in chemistry from the Johns Hopkins University and a Ph.D. in Marine Science from the College of William and Mary, School of Marine Science in 1996

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