Andy Hickner's blog

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 kate.nyhan@yale.edu.

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! 

Guides are unavailable

26 February 2016 - 11:10am by Andy Hickner

UPDATE:  Guides are back up.  Thanks for your patience.

The Library's Guides are temporarily offline due to technical problems with the vendor.  We have no further information at this time.  Stay tuned for updates.  

75 Years of Cushing/Whitney Medical Library: The Rotunda

16 February 2016 - 9:52am by Andy Hickner

(By Melissa Grafe)
 
The rotunda
 
Walk past the Circulation desk at the entrance of the Cushing/Whitney Medical Library and down the corridor displaying art from the Prints, Drawings, and Posters collection. Coming out of the corridor, you enter the Rotunda, the heart of the library.  The Rotunda of the Medical Library honors famed neurosurgeon and bibliophile Dr. Harvey Cushing (1869-1939).  When Cushing, along with Yale physiologist John Fulton and Swiss tuberculosis expert Arnold Klebs, joined their collections together, Cushing successfully advocated for a medical library at Yale.  Grover Atterbury, Cushing's classmate and friend since college, was selected as the architect, and brought “into reality Dr. Cushing’s dream of a great medical library.”  Designed in a Y, at the center of the library is the Rotunda, the gift of Cushing's Class of 1891, which was celebrating its 50th reunion.  Inscribed on one side of the Rotunda:
 
The Class of Yale 1891
Have Contributed to this Rotunda
In Affectionate Memory of Their Classmate
HARVEY CUSHING
Born in Cleveland Ohio, 8 April 1869
Died in New Haven Connecticut, 7 October 1939
 
The words below the balcony read:
This Rotunda is Dedicated to Harvey Cushing—Inspiring Teacher—Pathfinder in Neurosurgery —Master of the Science and Art of Healing
 
The crests just below the balcony are of 14 universities that awarded Cushing honorary degrees, including Oxford University and the University of Edinburgh. Eight exhibition cases showcased the Medical Historical Library’s collections, topics in medicine and medical history, and the history of the Medical School for nearly 75 years.  Medical students, faculty, researchers, alumni, and visitors since 1941 have crossed the grand seal on the floor, which incorporates parts of the seal of Yale University with a simple map of the Medical Library.  Many have also stood in the center of the seal and yelled out to experience the strange acoustics resulting from the design of the Rotunda and the colorful skylight directly above the seal.
 
For the Medical Library’s 75th anniversary, please consider giving towards the Rotunda’s restoration or other 75th anniversary projects.

Embase: A strong source for international and drug literature

4 February 2016 - 10:33am by Andy Hickner

Embase is a database covering international biomedical literature from 1974 to the present. All MEDLINE records are included in Embase, as well as over 5 million records not covered in MEDLINE.  Embase is especially strong in its coverage of drug therapy, pharmaceutical research, and medical devices. Embase also provides a global perspective in medicine, with coverage of journals published in 90 countries.

You can access Embase here or by clicking under "Highlighted Resources" on the Cushing/Whitney Medical Library homepage.  For Embase training or help, contact your personal librarian or your departmental librarian

Training Sessions for the Winter Semester at the Cushing/Whitney Medical Library

29 January 2016 - 3:41pm by Andy Hickner

The Cushing/Whitney Medical Library has prepared the following menu of training sessions for the winter semester. It includes training on how to do literature search, patent search, use of Cytoscape, genome browsers, EndNote, systematic reviews, functional analysis, variant annotation, and more. Since seating is limited, please register to reserve yours by following the links next to each session.

Please contact Vermetha Polite vermetha.polite@yale.edu for questions or comments on these sessions.

PubMed: Improve your Skills

Description:        PubMed is one of the most comprehensive resources for searching the biomedical literature.  Most researchers have used it at one time or another, but it may be time to brush up on your search skills to ensure that you a relevant set of results.  In this class, we will go over PubMed search techniques, including how to quickly limit a search and the role of Medical Subject Headings (MeSH) in creating more effective searches. Participants will also learn timesaving features such as saving searches and how to link out to full-text.

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Date & Time:      5:00pm - 5:50pm, Thursday, February 4, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1078963

 

Date & Time:      5:00pm - 5:50pm, Thursday, February 18, 2016

Registration Required:      http://schedule.yale.edu/event.php?id=1081044

 

Date & Time:      12:00pm - 12:50pm, Friday, February 26, 2016

Registration Required:    http://schedule.yale.edu/event.php?id=1081379

 

Date & Time:      5:00pm - 6:00pm, Wednesday, March 2, 2016

Registration Required:      http://schedule.yale.edu/event.php?id=1081440

 

Date & Time:      5:00pm - 5:50pm, Tuesday, March 22, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1081964

 

Date & Time:      5:00pm - 5:50pm, Wednesday, April 13, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1082069

 

RefWorks Basics

Description:        Learn basic features and use of this web-based citation management system, such as setting up a Yale account (no purchase required), exporting citations from external databases and importing them into your account, and using RefWorks with MS Word to create citations in context and bibliographies for your manuscripts. This class is one hour.

Date & Time:      12:00pm - 1:00pm, Wednesday, January 27, 2016

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Registration Required:     http://schedule.yale.edu/event.php?id=1078940

 

Managing your References with EndNote

Description:        EndNote is a citation-management software application that makes saving citations and then citing them within documents easy. EndNote's pre-formatted style templates, specific to journal instructions, make it easy to insert references into your papers as you write them. In this class you will learn how to easily add citations into your EndNote library, attach PDFs, and insert references into your research papers.

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Date & Time:      3:00pm - 4:00pm, Thursday, January 21, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1078930

 

Date & Time:      5:00pm - 6:00pm, Wednesday, January 27, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1078939

 

Date & Time:      2:00pm - 3:00pm, Friday, February 5, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1078961

 

Date & Time:      5:00pm - 6:00pm, Wednesday, February 10, 2016

Registration Required:      http://schedule.yale.edu/event.php?id=1078974

 

Date & Time:      5:00pm - 6:00pm, Wednesday, February 24, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1081369

 

Date & Time:      5:00pm - 6:00pm, Tuesday, March 8, 2016

Registration Required:      http://schedule.yale.edu/event.php?id=1081753

 

Date & Time:      2:00pm - 3:00pm, Wednesday, March 16, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1081767

 

Date & Time:      1:00pm - 2:00pm, Friday, March 25, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1081922

 

Date & Time:      5:00pm - 6:00pm, Thursday, April 7, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1082066

 

Date & Time:      5:00pm - 6:00pm, Wednesday, April 27, 2016

Registration Required:    http://schedule.yale.edu/event.php?id=1082070

 

Enhance your Library Skills

Description:      Are you new to the Medical Campus? Need a refresher on how to use the Medical Library?  Information experts will assist you in finding everything from books in the online catalog to locating peer-reviewed full-text articles including when and how to request materials through our Interlibrary Loan service. You will be surprised about the resources and services available to you.

Use the library catalog to find materials including books, prints, maps, and more

Decipher confusing citations

Find full-text articles

Identify article databases in your subject area

Distinguish when and how to request material through Interlibrary Loan

Identify your librarian

Date & Time:      2:00pm - 2:50pm, Thursday, January 28, 2016

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Registration Required:     http://schedule.yale.edu/event.php?id=1078941

 

Tools for gene enrichment analysis

Description:                        Bioinformatics enrichment tools play an important role in identifying, annotating, and functionally analyzing large list of genes generated by high-throughput technologies (e.g. microarrary, RNA-seq, ChIP-chip). This workshop will provide an overview of the principle, type of enrichments, and the infrastructure of enrichment tools. By using concrete examples, it will also introduce some of the most popular tools for gene enrichment analysis such as DAVID, GSEA, and WebGestalt, as well as the proprietary softeare MetaCore.

Date & Time:      12:00pm - 1:30pm, Thursday, February 4, 2016

Location:              SHM L Simbonis Room 101A Yale Medical Library, 333 Cedar St. New Haven CT 06520

Registration Required: http://schedule.yale.edu/event.php?id=1063877

 

Systematic Reviews: Conducting comprehensive searches

Description:        One critical step in the SR process is to comprehensively search the literature. This workshop will introduce procedures to ensure that your search is comprehensive, methodical, transparent and reproducible.

Date & Time:      1:30pm - 3:00pm, Wednesday, February 10, 2016

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Registration Required:      http://schedule.yale.edu/event.php?id=1081041

 

The VERY Basics of the Unix Command Line

Description:        A lot of biomedical software programs do not come with a graphical user interface (GUI), and a Unix command-line terminal environment is required to run such programs. In this 2-hour session, you will learn the basics of a Unix command-line terminal, such as how to navigate the file system, the permission and security structure, and how to run programs from the command line. No previous Unix or command-line experience is required to attend this session.

Free and open to any Yale University student, faculty and staff. 

Registration required since the number of seats is limited.

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Date & Time:      2:00pm - 4:00pm, Thursday, February 11, 2016

Registration Required: http://schedule.yale.edu/event.php?id=1081054

 

Date & Time:      10:00am - 12:00pm, Thursday, April 14, 2016

Registration Required:     http://schedule.yale.edu/event.php?id=1082074

 

Introduction to patents and patent searching

Description:        Patents are challenging but important sources for product development and discovery of technical information. This workshop will provide a basic introduction to the patent literature and the United States patent process. We will look at tools and strategies for locating patents and intellectual property.

Date & Time:      2:00pm - 3:00pm, Friday, February 19, 2016

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Registration Required: http://schedule.yale.edu/event.php?id=1088303

 

Introduction to Genome Browsers

Description:        In this workshop we will learn how to navigate the genome browsers from NCBI's Genome Workbench, UCSC Genome Browser, and Ensembl. These browsers are valuable tools when identifying, localizing genes, and looking at their information in the genomic context. By using concrete examples, it will be shown how to locate a human gene, download a gene sequence and its upstream sequence, locate Single Nucleotide Polymorphisms (SNPs) and conserved regions, and use the browsers to download results in a batch

Date & Time:      12:00pm - 1:30pm, Thursday, February 25, 2016

Location:              Medical Library, Simbonis Large Conference Room 101A, 333 Cedar St, New Haven CT 06520

Registration Required: http://schedule.yale.edu/event.php?id=1063872

 

Cytoscape: Going from Raw Data to a Publishable Image

Description:        These hands-on workshops will demonstrate the use of Cytoscape, an open source molecular interactions visualization tool. Cytoscape allows for the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.  One session, “Cytoscape:  Going from Raw Data to a Publishable Image,” will cover core functions, such as learning how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, manually add nodes/edges, etc.

Date & Time:      9:00am - 12:00pm, Thursday, March 3, 2016

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

Presenter:          Marci Brandeburg, University of Michigan.

Registration Required: http://schedule.yale.edu/event.php?id=1048510

 

Cytoscape apps with a Focus on MetScape

Description:        This hands-on workshop will provide an introduction to Cytoscape apps, which add functionality to the core software.  It will focus on a specific app example, MetScape, which is used to visualize and interpret metabolomics and gene expression data in the context of human metabolic networks.  A brief introduction to other apps, such as MCODE (cluster finding tool), SocialNetwork (builds co-publication networks), and MetDisease (annotates metabolic networks with MeSH disease terms) will be included.

Date & Time:      1:30pm - 4:00pm, Thursday, March 3, 2016

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

Presenter:          Marci Brandeburg, University of Michigan

Registration Required: http://schedule.yale.edu/event.php?id=1048558

 

BioMart: A Research Data Management Tool for the Biomedical Sciences

Description:        Some complex biomedical questions cannot be answered by reading the published literature. These may require aggregation of data from several data sets. In this regard, BioMart (www.biomart.org) is a freely available open source system that allows complex queries across more than 40 different biological data sets through a single web interface. Originally developed for the Ensembl genome browser, BioMart has been integrated into widely used software such as Galaxy, BioConductor, and Cytoskape. The BioMart interface is also used by data portals such as Ensembl, Wormbase, Gramene, and Reactome.

 

In this workshop we will use simple examples to demonstrate how to navigate, build queries, and save and export the results on BioMart such as:

- how to retrieve the Ensembl mouse genes and genomic locations in the first 10 Mbp of chromosome 1 region;

- retrieving 1 kb of upstream sequences from a cluster of human genes identified by an expression profile experiment;

- obtain a list of the SNPs that have been associated with RB1. For the SNPs, obtain several attributes such as source, rs ID, chromosome location, and pathogenicity

 

Date & Time:      12:00pm - 1:30pm, Thursday, March 10, 2016

Location:              Medical Library, Simbonis Large Conference Room 101A, 333 Cedar St, New Haven CT 06520

Presenter:          Rolando Milian

Registration Required: http://schedule.yale.edu/event.php?id=1063879

 

Novel Online Tools for Mining the Biomedical Literature

 

The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools that make use of Natural Language Processing Algorithms and data visualization (e.g. CoreMine, NextBio, Semantic MEDLINE, etc) may be of help when sorting through this abundance of literature as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions and generating/narrowing hypothesis.

Date:     Thursday, March 24, 2016

Time:     12:00pm - 1:30pm

Location:              Cushing/Whitney Medical Library at Yale University, Simbonis Conference Room 101A, 333 Cedar St, New

Presenter:          Rolando Milian

Registration Required: http://schedule.yale.edu/event.php?id=1063880

 

My Bibliography and SciENcv: grant reporting, compliance and biosketch through MyNCBI

Description:        Although not required at this point, the NIH suggest the use of the Science Experts Network Curriculum Vitae (SciENcv), -a MyNCBI online tool- that serves as an interagency system designed to create biosketches for multiple federal agencies. This, along with the use of My Bibliography for grant activity reporting and NIH Public Access Policy compliance, increases the importance using MyNCBI as a tool for managing NIH-sponsored research. This workshop introduce researchers, research assistants and administrators on the effective use of these online tools and will cover the following among other topics:

How to create MyNCBI account and how to link it to the eRA Commons account

How to delegate your account

 How to populate and manage My Bibliography

How to use My Bibliography for grant reporting/compliance

How to use SciENcv to create different biosketches (from scratch, from external source, etc)

How to create and ORCID ID* and how to link SciENcv to that ORCID ID

 

*ORCID stands for Open Research and Contribution ID. Some publishers and journals (Springer, Wiley, Journal of Neuroscience, The Journal of Immunology, etc.) are asking authors to submit their ORCD ID along with their manuscripts for publication.

 

Date & Time:      12:00pm - 1:00pm, Thursday, April 21, 2016

Location:              Medical Library, Room 103 TCC, 333 Cedar St, New Haven CT 06520

Presenter:          Rolando Milian

Registration Required: http://schedule.yale.edu/event.php?id=1063884

 

 

 

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