General Library News

Fair Use Week

Celebrate Fair Use Week (February 25 - March 1) with Yale University Libraries! "The week highlights the many uses relying on fair use and helps to inform our academic communities and the public at large about this exception created in the U.S. Copyright Act of 1976. Fair use is described in §107 of the Act and may be used judiciously upon undertaking analysis of the section's four factors: Purpose of the use; Nature of the work being used; Amount of the original work used; and whether there is an effect on the Marketability for the original copyright holder. This clause in the law allows all individuals the right to use copyrighted works without permission of the copyright holder IF the user, after reasonable assessment of the four factors, finds that the use weighs in favor of fair use. For more information about fair use and undertaking a fair use analysis, see the fair use tab in this Research Guide under Using Copyrighted Works and the Fair Use Analysis tool also found on the office of General Counsel's Rights Clearance for Digital Projects." The Cushing/Whitney Medical Library will be hosting a fair use popup table on Tuesday, February 26th from 11:30am - 1:30pm. Stop by and learn about fair use and its importance in our community! For a full list of events, please see this page: https://guides.library.yale.edu/copyright-guidance/fair_use_week

Love Data Week 2019 at CWML

February 11 - February 15 Love Data Week aims to raise awareness and build a community to engage on topics related to research data management, sharing, preservation, reuse, and library-based research data services. Learn about and register for data related programing run through the Cushing/Whitney Medical Library below. If you have any questions about Love Data Week at CWML, please email Sawyer Newman at medicaldata@yale.edu. 1. Research Data Management for the Health Sciences Monday, February 11 10:00 am - 11:00 am, TCC Data, data everywhere, but not a drop is usable. ~Rime of the Modern Researcher Are you a modern researcher? The current capabilities for collecting and generating large data sets mean researchers need to know how to manage their data as a part of their research process. This workshop will overview research data and research data management while providing examples of strategies to keep data findable, accessible, interoperable, reusable (FAIR), and protected. 2. Data Collection Software Demonstration: The REDCap Connection Tuesday, February 12 10:00 am - 11:00 am, TCC REDCap@Yale REDcap is an electronic data collection system that can be used to collect and securely store large datasets. It is very useful to researchers and widely used throughout the Yale School of Medicine, Public Health, and Nursing Schools. Get connected and learn about this great system: what it is, how it is used, why is needed, and how it relates to other data collection systems being used at Yale. If you have any questions about this session, please email medicaldata@yale.edu. 3. Functional Analysis of Omics Data with Metacore Wednesday, February 13 10:00 am to 12:00pm, C-103 MetaCore is an integrated software suite for functional analysis of Next Generation Sequencing, variant, CNV, microarray, metabolic, SAGE, proteomics, etc. MetaCore is based on a high-quality, manually-curated knowledge base. In this session we will learn how to search the knowledge base and do overrepresentation analysis to identify and learn about the functional significance (relevant pathways, networks, and diseases) of a list of differentially-regulated molecules. The Medical Library provides free access to this online software for Yale affiliates. Please register for a MetaCore account before attending this session. If you have any questions about this class, please email Rolando Garcia-Milian at rolando.milian@yale.edu 4. Excel 2 Wednesday, February 13 10:00 am - 12:00pm, TCC Excel is a commonly used spreadsheet software, but you may not be taking full advantage of its features. The target audience for this two hour class is Excel users who have the basics down, and who are ready to be introduced to some of Excel’s more advanced features. Topics will include formulas (including IF, COUNTIF, VLOOKUP), pivot tables for data summarization, and conditional formatting. 5. Data Services Meet and Greet Thursday, February 14 1:30 pm - 4:30 pm, Hallway outside of the CWML Cushing Whitney Medical Library Data Support Services Learn about the Cushing Whitney Medical Library can help you with your research data through consultations, workshops, and resources, and meet the Data Librarian for the Health Sciences. Towards a Yale Data Initiative - Introducing Yale Center for Biomedical Data Science A brief introduction will be provided to the Yale community on the Center for Biomedical Data Science, including our missions, objectives, members, seminars, training events, web presence, and more. Yale Open Data Access (YODA) Project Come meet and greet the YODA team at Yale. Through experience and input from the public and stakeholders, the YODA Project has iteratively developed a model to make data available to researchers in a sustainable way, in which data sharing becomes a part of the clinical research enterprise of the future. The mission of the YODA Project is to not only increase access to clinical research data, but to promote its use to generate new knowledge. 6. Introduction to R with Swirl Friday, February 15 10:00 am - 11:00 am, TCC R is a powerful programming language that can be used for collecting, cleaning, manipulating, analysing, and visualizing your data. This class will show you how to use the Swirl package to help you teach yourself the basic functions of R. This workshop is designed for those who have never used R previously, and there will also be the opportunity to learn about more advanced tutorials and resources available to you at the end of the workshop. 7. Introduction to Google Analytics Friday, February 15 1:30pm - 2:30pm, TCC Join our Web Services Librarian for a hands-on workshop that will demonstrate how you can use Google Analytics to better understand your website users. This workshop will cover account setup, code snippet installation, the Google Analytics Dashboard, acquisitions, user behaviors and understanding the audience of your website. If you have any questions about this class, please email dana.haugh@yale.edu

Endangered Data Week 2019 at CWML

February 25 - March 1 Endangered Data Week strives to shed light on public datasets that are in danger of being deleted, repressed, mishandled, or lost. Learn about and register for this special programming through the Cushing Whitney Medical Library. If you have any questions about Data Week at CWML, please email medicaldata@yale.edu. 1. Research Data Management for the Health Sciences Monday, February 25 10:00 am - 11:00 am TCC Are you a modern researcher? The current capabilities for collecting and generating large data sets mean researchers need to know how to manage their data as a part of their research process. This workshop will overview research data and research data management while providing examples of strategies to keep data findable, accessible, interoperable, reusable (FAIR), and protected. 2. RSpace Electronic Lab Notebook (ELN) Demonstration Monday, February 25 9:30 am - 10:30 am, and 2:00 pm - 3:00 pm Location: Anlyan Center TAC N203 Conference Room Guest presenters: Rob Day (Director of Sales at RSpace) and Rory Macneil (CEO and Cofounder at RSpace) The RSpace ELN is designed for labs that want to transition to a compliant and secure documentation platform, but need something that’s intuitive and easy to use. Something that everyone can get started with quickly, and the PI can use to keep tabs on what’s happening in the lab. Through the demo you will learn how to get started, see options for organizing your lab group, understand sharing and collaboration, be introduced to document and template creation, managing and annotating images, support for chemistry, and learn how to set up and take advantage of the many optional integrations like those with protocols.io, OneDrive and Google Drive. RSpace has some powerful capabilities in the following areas: Flexibility: RSpace doesn’t force you into a limited number of restricted workflows; it gives you tools to enhance your existing workflows. Traceability: Linking and unique IDs, added to powerful search capability, simplify finding data and documents and relations between them. Connectivity: RSpace is interoperable with a wide range of general purpose and science-specific tools, including file storage apps OneDrive, Google Drive, Box and Dropbox, tools like protocols.io, Github and Slack, and data repositories like Figshare and Dataverse. It’s easy to get data out of RSpace in a variety of formats, e.g. pdf, html and xml, so you’ll never be locked into RSpace. If you have any questions before the class, please email medicaldata@yale.edu 3. Using Covidence to Improve your Systematic Review Workflow Wednesday, February 27 9:30 - 10:30 am Location: TCC If you are a student, faculty, or researcher working on, or planning to work on a systematic review - this class is for you! From screening to data extraction, this online tool helps streamline the systematic review process. Come learn how Covidence can help you manage the large quantities of citation data data associated with conducting a systematic review. 4. Data Analysis Using Qlucore Omics Explorer Thursday, February 28 10:00 am - 12:00 pm Location: C-103 Qlucore tools enable researchers to quickly visualize, analyze and perform biological exploration (e.g. GSEA) on various data including RNAseq, microarrays, proteomics, miRNA, methylated DNA, metabolomics, lipidomics, mulitplex and FACS data, clinical data, biomarkers, etc. If you have any questions about this class, please email Rolando Garcia-Milian at rolando.milian@yale.edu 5. Data Discussion: Touring the Cushing Center and the Cushing Tumor Registry Thursday, February 28 11:00 am - 12:00 pm Location: Meet in the lobby of the Cushing/Whitney Medical Lobby “The brains are so cool!” All our visitors say that - but have you heard the story of how this collection came to be, and how researchers are still using these samples today? For Endangered Data Week, we’re offering this special tour exploring how Cushing Tumor Registry has survived a century, and still supports research today. The Cushing Tumor Registry was endangered when researchers moved institutions, when key staffers retired or died, when funding streams dried up, and when environmental conditions threatened preservation. Could this happen to your project? Join Cushing Center Coordinator Terry Dagradi and Research and Education Librarian Kate Nyhan to discuss the continuing life of this extraordinary (and at one time, endangered) collection. 6. Introduction to R with Swirl Friday, March 1 10:00 am - 11:00 am Location: TCC R is a powerful programming language that can be used for collecting, cleaning, manipulating, analysing, and visualizing your data. This class will show you how to use the Swirl package to help you teach yourself the basic functions of R. This workshop is designed for those who have never used R previously, and there will also be the opportunity to learn about more advanced tutorials and resources available to you at the end of the workshop.

New year, new classes!

You may already know that the library often teaches workshops on EndNote and PubMed, but there is a lot more going on in our teaching spaces these days. This post will highlight five new events you’ll see popping up on the calendar more frequently. Head to the calendar to sign up! Introduction to R with Swirl with Sawyer Newman Learn about installing R, RStudio, and practice R using the R library Swirl! This hands-on workshop is for those who have no experience in R. After a brief introduction and demonstration in R, participants will work on self-guided exercises using the Swirl package. Research Data Management for the Health Sciences with Sawyer Newman Does your research involve data? This workshop will overview research data and the management of research data while providing examples of strategies you can take to make your data easier to navigate, understand and more secure. Introduction to Cytoscape for the analysis, visualization, and integration of data with Rolando Garcia-Milian Cytoscape is an open source platform for analysis and visualization of networked data, molecular interaction networks, and biological pathways. It also allows integrating these networks with annotations, gene expression profiles and other types of data. The workshop covers getting started in Cytoscape, creating and merging networks, visualization, installing add-on applications and more. Mobile App Mondays with Alyssa Grimshaw Mobile App Mondays are drop-in times to learn about the library’s extensive collection of free mobile applications, troubleshoot problems, and see a demonstration of the weekly featured application. Walk-in Wednesdays with Caitlin Meyer (mornings) and Alyssa Grimshaw (evenings) Walk-in Wednesdays are your opportunity to drop by with questions about databases, citation management, searching the literature, or whatever else is on your mind. Have an idea for a new class? Email Caitlin Meyer.

Resource Spotlight: Global Health

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at Global Health. Produced by CABI, an international not-for-profit organization focused on solving problems in agriculture and the environment, Global Health is the premier resource for public health information. Global Health aims to comprehensively cover public health-oriented topics including biomedical life sciences, chronic diseases, disease diagnosis and therapy, environmental and occupational health, epidemiology and biostatistics, health promotion and wellness, health systems, infectious and vector-borne diseases, nutrition, public health emergencies, tropical and international health, and more. Though PubMed and Embase may be the go-to resources for a lot of biomedical research, Global Health offers access to thousands of journals that are indexed in neither database. Furthermore, Global Health includes international publications and grey literature sources (proceedings, theses, reports, electronic-only publications), meaning researchers are able to access information on an issue from many perspectives and publication types. Finally, another distinguishing characteristic of Global Health is its editorial policies. Entrance into the database is governed by subject specialists who select relevant papers. Publications from more than 100 countries are reviewed for inclusion, and non-English papers deemed relevant are translated to broaden access to that research. At Yale, you can access Global Health through the OvidSP platform. Ovid offers an intuitive search experience that lets you build complex literature searches line by line. You also can save searches and set up automated email alerts, so you can stay up to date on a topic with relatively little work. For questions on how to best use Global Health, please contact Kate Nyhan.

Common EndNote for Mac issues and how to solve them

EndNote X8 on Mac computers can be finicky. We've collected some common issues Apple users experience and figured out how to solve them. If you are still struggling to get EndNote working well after you work through this page, feel free to sign up for an EndNote class, check out our EndNote tutorials, visit the walk-in IT help desk on the lower level of the medical library, or contact EndNote support. “When I try to download the software, my computer says it can’t download it because it’s from an ‘unknown developer’!” Open up System Preferences, then Security & Privacy, navigate to the General tab, and click “Open Anyway”. Proceed with download and install. “When I download citations, the computer says it doesn’t have an application to open that type of file!” Temporary solution: Click “Choose Application” -> EndNote x8 -> EndNote x8 Permanent solution: Open your Downloads folder and right click on the downloaded file. Click “Get Info”. Scroll down to “Open with”, select EndNote, and then click “Change All…”. Now, whenever you download a file with that extension, your computer will know what to do. Common citation file extensions are .nbib, .enw, .cgi, .ciw, and .ris, so you may have to do this multiple times depending on where you like downloading files from. “When I try to open a downloaded file of citations, I get a weird pop-up telling me to choose a library. Even weirder, sometimes it says ‘This library is in use by somebody else’!” I’ve had luck bringing my EndNote library back up on the screen and then opening my downloaded file. If the library is minimized or if you’d exited out of EndNote, these problems may occur more often. “When I use Find Full Text, it isn’t finding anything, says ‘Searching…’ forever, or freezes my computer!” 1. Connect Find Full Text to library resources. Go to EndNote in the upper left-hand corner -> Preferences -> Find Full Text -> then type http://wa4py6yj8t.search.serialssolutions.com in the OpenURL Path box. 2. Were you connected to the Yale Guest network at any point today? Exit out of EndNote, make sure you’re connected to Yale Secure, open EndNote, try again. “When I open Word to start writing, I don’t see EndNote as an option!” Go to EndNote, click on EndNote in the upper left-hand corner, and click Customizer. Next to Cite While You Write in the list of components, check the box to install the plug-in. The progress bar may get to the end and the window won’t close. If this happens, force quit EndNote and then restart EndNote and Word. It should work now. “When I try to insert a citation in Word, the ones I’m looking for don’t come up!” Make sure you’re hitting enter after you type an author’s name. If it’s still not working, in Word on the EndNote tab, select Preferences, then Application, then make sure “EndNote” is selected – not “EndNote online.” “When I try to open my EndNote library, it says it’s corrupted or that it can’t open it!” When you create an EndNote library, you also create a .Data folder with the same name. The .enl library file and the .Data folder need to be kept in the same place, or else the library can’t open. “When I try to import PDFs I already have on my computer, I’m not having much luck!” In EndNote, select File then Import. Select Options, then in Import Options select PDF File or Folder. If you have had any other problems you've encountered and solved, and think they would be helpful additions to this list, contact Caitlin Meyer.

Fall Class Highlights

Are you looking to brush up on your basic literature searching skills? Trying to use PubMed or EndNote and encountering difficulties? Need to set up SciENcv? Our fall workshop calendar has everything you may need and more for a productive fall term. Read on for details or head straight to the class calendar. In addition to weekly PubMed and EndNote classes, here are some of the classes coming up this fall that any member of the Yale community is welcome to register for and attend: Basic Library Classes Free resources and support in support of research Second Tuesdays at noon Have you ever wondered what services and resources the library provides to help you with your research? In just 20 minutes, you’ll learn about first-class bioinformatics software, specialized databases, support for grant compliance, systematic review searching, statistics consultants, and more! Academic Job Search Series at Cushing/Whitney Medical Library The Cushing/Whitney Medical Library is excited to participate in this year’s Academic Job Search Series in partnership with the Office of Career Strategy, the Center for Teaching & Learning, and the Graduate Writing Lab. Tools for Keeping Current & Staying Organized October 4th Expand your toolkit for keeping current with the literature in your field and staying organized during the job search process. This session will cover: setting email alerts in various databases, setting up EndNote as a personal database, and using Trello to track job applications throughout the process. My Bibliography and SciENcv: grant reporting, compliance, and biosketch through MyNCBI October 11th Learn how to create a MyNCBI account and link it to eRA Commons, delegate your account, populate and manage My Bibliography, learn how to use SciENcv to create multiple biosketches, create an ORCID, and more! Special Topic Classes Excel 1 & Excel 2 September 18 & October 4 In part one, refresh your basic Excel skills and move onto some intermediate topics such as formatting spreadsheets, sorting, filters, text-to-columns, combing data, and trimming. In part two, learn advanced functionality such as IF, COUNTIF, VLOOKUP, pivot tables, and conditional formatting. Creating Surveys with Qualtrics September 20 Qualtrics is a web-based tool provided by Yale ITS to create surveys. This hands-on class will prepare you to create your own online survey using the Qualtrics user-friendly interface. By the end of the class you will be able to: create a survey with multiple question types, distribute the survey in various ways, and view/analyze results.

Resource Spotlight: Ingenuity Variant Analysis

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at Ingenuity Variant Analysis (IVA). IVA is a web-based tool that combines analytical tools and content from the Ingenuity Knowledge Base to help identify disease variants in human sequencing data. The product allows you to select multiple samples to analyze together. From there, you can design the forthcoming analysis and add any relevant biological terms to help narrow down the list of variants likely contributing to the disease or phenotype at hand. IVA supports a range of upload formats, including Variant Call Format (VCF), Genome Variation Format (GVF) and Complete Genomics files (Var, MasterVar, High confidence junction, etc.). After you have set up your data, IVA lets you interact with the data with a series of customizable filters. Some of the filter types include: biological context, genetic analysis, predicted deleterious, cancer driver, pharmacogenetics, and more. Keep an eye on the library’s class calendar for trainings on IVA and all bioinformatics-related software. In the meantime, Qiagen, the company that produces IVA, has produced webinars, tutorials, and guides to help you get started. Finally, please note that the library’s license to IVA is for academic and research use only. Results may not be incorporated into a diagnostic product or service. Request an IVA account. For questions on how to best use IVA, feel free to contact Rolando Garcia-Milian.

Finding Conference Proceedings

Despite the promise of tools like Quicksearch and the breadth of massive databases like Scopus, certain types of information simply cannot be found in one place. No need to fret, though! We've got you covered. This series of blog posts will serve as a home of recommended resources and searching tips for hard-to-find types of information. Have a suggestion for a subject? Shoot me an email! Conference proceedings – the collections of papers and/or abstracts that are presented at conferences – may be published in book format, as special issues of a journal, or as a serial. Sometimes they are in the format of an abstract, sometimes in the form of a ‘conference paper’. A conference paper may morph into a journal article (usually with substantial additional material) but not always. If a conference abstract is found, then further sleuthing is required to see if the organization supporting the conference published proceedings or stopped at abstracts only. You might do an author search in the following resources to see if the author followed up the conference abstract or paper with a full-length journal article: PubMed, Web of Science, Scopus, Embase, or Google Scholar. Last resort? Contact the author/researcher directly and ask! Recommended Resources Conference Proceedings Citation Index (Web of Science) Click on ‘More settings’ to restrict your search to specific conference proceedings citation indices or search the entire Web of Science Core Collection. Embase Limit to publication types: conference abstract, conference paper, or conference review. ProceedingsFirst (OCLC) This is an index of worldwide conference proceedings – every published congress, symposium, conference, exposition, workshop and meeting received by the British Library Document Supply Centre. WorldCat This ‘world catalog of publications’ is an excellent tool for finding conference proceedings. Search specific conference number and title (16th and “international AIDS conference”), limit by year(s): 1989 or 1990 or 1991 Tips & Tricks Associations usually publish abstracts from their Annual Convention in the association journal in the same issue or special supplement every year. Sometimes both the authors and the title will change when published as a full-length journal article. Make sure to search creatively and read carefully. Society, organization, and association websites frequently have information about their publications, including proceedings and annual meeting abstracts. Requesting conference proceedings through Interlibrary Loan may take longer than traditional requests. It may only ever be available as an abstract (see second bullet point).

Resource Spotlight: Scopus

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at Scopus. Scopus is the single largest abstract and citation database of peer-reviewed literature. Unlike Medline resources like PubMed and Ovid MEDLINE, Scopus is also the home to non-journal literature, like conference abstracts and books. Indexing more than 22,000 journals, Scopus covers science, technology, medicine, social sciences, arts, and humanities - making it a great resource for interdisciplinary projects. Scopus’ user-friendly interface mimics Google search in its simplicity. No special syntax or subject headings are needed to conduct an initial search. Being an academic resource, though, Scopus offers many functionalities that Google does not: Author search and author profiles Search by affiliation to gauge the output of a specific school or department The ability to search for certain document types Optional advanced search functionality that lets you search specific fields like chemical or biological entities, editors, funding information, conference information and more Offering data at the article, journal, and author level, Scopus’ broad range of content coverage makes its research impact information robust as well. Users can easily disambiguate authors and navigate to author profile pages that list publications, frequent collaborators, h-index, citation counts, disciplines that the author publishes in, and more. As mentioned above, this level of granular information is also available at the article and journal level. Scopus is a great place to start your research, a necessary inclusion in most systematic reviews, and a massive time-saver in calculating h-indices. With something to offer for students, clinicians, researchers, administrative staff and more start exploring Scopus today! For questions on how to best use Scopus, feel free to contact Research & Education Librarian Caitlin Meyer.