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Sawyer Newman's blog

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

6 November 2019 - 2:25pm by Sawyer Newman

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

5 July 2019 - 9:29am by Sawyer Newman

As a quick reminder, PubMed contains citations for biomedical literature that users can access through the library here. 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:   Learn how to find data in PubMed, PubMed Central at the Medical Library’s data services site: https://library.medicine.yale.edu/research-data/find-datasets/   This post is a summary of an NLM video titled Data Discovery in PMC and PubMed. You can view the full presentation by following this link.    

Access a DataCamp Trial through the CWML & Join Drop-in Sessions

19 February 2019 - 3:14pm by Sawyer Newman

Information about the Medical Library’s Access to Data Camp The Medical Library has access to a limited trial version of DataCamp, a web platform for learning topics in data science. Participant enrollment in DataCamp through the library will provide access to DataCamp’s self-directed exercises in data science including R, Python, Git and SQL.   This classroom is being offered as a limited trial for 50 participants, who will have access to the DataCamp classroom until the end of June.   Disclaimers: There is a limit of 50 participants, invitations will be sent out on a first come, first serve basis, and requestors will be responsible for completing the enrollment. This trial will end at the end of June 2019, and participants will lose access to DataCamp at this time. Because of the scope of offerings through DataCamp classes, it is not guaranteed that the Data Librarian on hand will be able to troubleshoot every problem encountered, and it is expected that as a part of this education model, participants work towards self-directed learning. Participant data about progress through courses and exercises are collected by DataCamp. This data will be de-identified and used by the Medical Library to inform future education services offered by the library. If you would like more details about what information is collected that the library will be able to see, please email medicaldata@yale.edu.   Information about CWML DataCamp Drop-in Sessions Time: 12:00 - 1:00pm Days: Fridays during the Spring 2019 semester  Location: Cushing/Whitney Medical Library Room 101a During this hour, enrollees in the Medical Library’s DataCamp portal are welcome to drop-in to work through DataCamp exercises in the library’s meeting room 101a, discuss any encountered problems, and to receive support for the DataCamp tool from the Data Librarian.  

2019 Data Weeks at the CWML

6 February 2019 - 8:51am by Sawyer Newman

  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. Love Data Week programming through the CWML - view the of events Official Love Data week - visit the website 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. Endangered Data Week programming through the CWML - view the list of events Official Love Data week - visit the website   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

6 February 2019 - 8:32am by Sawyer Newman

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. Register for this class here   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. Register for this class here   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. Register for this class here 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.   Register for this class here   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. Register for this class here   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 Register for this class here

Endangered Data Week 2019 at CWML

6 February 2019 - 8:28am by Sawyer Newman

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. Register for this class here 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 Register for the 9:30 am - 10:30 am session here Register for the 2:00 pm - 3:00 pm session here   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.   Register for the class here 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. Register for this class here 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. Register for this tour here   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. Register for this class here  

DOI/Persistent Link Creation Through Yale ITS

10 December 2018 - 8:52am by Sawyer Newman

Did you know that Yale ITS offers a persistent linking service?  Persistent linking is available to anyone in the Yale community with an active NetID at no cost to the requestor. A DOI is a unique identifier that provides a persistent link to an object on the Internet. This persistant linking service can be used to create DOIs.  Learn more about this service through ITS here.  Place a request to create or update a persistant link here.   What are DOIs? DOI stands for Digital Object Identifier, which refers to the digital identifier of an object. Objects in this case can be any entity that is physical, digital, or abstract. DOIs themselves, are alphanumeric strings tied to a metadata description of the object, and a digital location.   What do DOIs do? DOIs provide persistent links to digital objects or information about physical objects that allow for easier data sharing and citation. Where standard URLs might change or break, a DOI is a persistent link that will not change.   What can I assign a DOI to? DOIs can be assigned to anything that has a URL or a specific location on the web. DOIs have been assigned to: Preprints Datasets Journal articles Technical reports Data visualizations (graphs)   Where else can I link a DOI to a dataset? DOIs can be assigned to datasets when they are deposit into data repositories such as figshare, Zenodo, or Dryad. Crossref provides DOIs and curates information (metadata) about its DOI’d objects in order to increase findability.  
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