Sawyer Newman's blog

NIH Living Textbook of Pragmatic Clinical Trials: New Content on Research Data

The Living Textbook of Pragmatic Clinical Trials is a collection of knowledge from the NIH Health Care Systems Research Collaboratory. This free web-accessed resource reflects a collection of special considerations and best practices in the design, conduct, and reporting of pragmatic clinical trials and is organized to follow the linear progression of these stages. Within this resource, special attention is nowgiven to the utilization and redistribution of research data by having dedicated sections on: Assessing fitness for use of real-world data sources (i.e., determining the applicability, quality and provenance of a dataset) Acquiring real-world data Data sharing and embedded research As of January 2021, the Living Textbook added information on using claims and CMS files. See the announcement and a list of added topics here. Other data types covered include, electronic health records (EHRs), administrative claims, patient-reported outcomes (PROs), patient-generated health data (PGHD), medical product/device registries, condition-specific or disease registries, and environmental factors / social determinants of health. Learn more about these topics, and additional topics covered by the NIH Collaboratory Living Textbook of Pragmatic Clinical Trials by utilizing this textbook here.

SPARC’s Federal Data Sharing Policy Resource Update Released

SPARC (the Scholarly Publishing and Academic Resources Coalition) has launched an update to its Federal Data Sharing Policy Resource. This update distills the latest changes in the US federal agencies’ data sharing policy requirements to make them more easily and quickly understandable. SPARC works to enable open sharing of research outputs and educational materials in order to democratize access to knowledge. This update supports open data by providing clear and compiled information on data sharing policies put in place by federal level funding organizations. From the SPARC news release, “This integrated policy resource can be used by researchers, librarians, policy makers, and other stakeholders to explore and compare agency plans for sharing articles and data. This analysis provides a tool for tracking practical information that can be used by active or prospective grant awardees to understand when, how, and where they need to make their research results accessible.” For each federal agency included in the list, SPAC details policy goals, how data are to be publicly shared, metadata and documentation to be included with the data, data citation and attribution standards, data management plan recommendations, compliance measures, and more. To interact with and learn from this resource, go here: https://sparcopen.org/our-work/sparc-federal-article-data-sharing-policy-resource/# Learn more about support at the Cushing/Whitney Medical library for: Scholarly Communication: https://library.medicine.yale.edu/scholarly-communication Research Data: https://library.medicine.yale.edu/research-data

November: National Awareness Month for Alzheimer’s Disease and Home Health Care

The bubble plot shown on this page (you may have also noticed it on the Medical Library’s digital signage and webpage banner), was created using ggplot2 in R. It shows publications related to Alzheimer’s Disease, Family Caregivers, and Home Health Care that has been cited more than 40 times by other research efforts. Follow the link here to interact with this graph, and view more details about each of the publications represented in this visualization. If you have any questions about this graph, please email medicaldata@yale.edu.

Finding Associated Data in PubMed and PubMed Central

As a quick reminder, PubMed contains citations for biomedical literature that users can access through the library. PubMed Central (PMC) is a free full-text archive of biomedical and life sciences journal literature. For more information about the differences between PubMed and PubMed Central, refer to this article. Until relatively recently, PMC was curated in a way archival collection of journal articles that allowed the use of found literature to discover more related research literature. In other words, articles have been linked to other articles, as illustrated below. However, research publications have become more complicated than article to article relationships can represent. Individual articles can be made up multiple resources including peer review statements, data, and code in addition to other related articles. See this illustrated below. To achieve this model, which will enhance the findability of research efforts alongside literature, NLM links associated data to publications via PubMed Central and My NCBI, which can could be presented in any or all of the three following forms:

2019 Data Weeks at the CWML

Be on the lookout for Data-themed classes, blogs, demonstrations, and programming during the following weeks at the Cushing/Whitney Medical Library! Love Data Week Monday, February 11 - Friday, 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. Endangered Data Week Monday, February 25 - Friday, March 1 Endangered Data Week strives to shed light on public datasets that are in danger of being deleted, repressed, mishandled, or lost. If you have questions about the the Data Weeks or would like to receive messages about Data Weeks events by the CWML, please email Sawyer Newman at medicaldata@yale.edu.

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.