Section outline

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  • Wednesday, January 5, 2022; 11:25 AM - 12:50 PM

    Lecture: Overview of UCSF Research Data and Resources


    Faculty: Eugenia Rutenberg, Rick Larsen, Angela Rizk-Jackson 

    • Course Introduction: 

      Individual introductions and discussion about the course, expectations, definitions and terms, student input. The lecture should be viewed beforehand. 

      Lecture topic questions: 

      • What is informatics research? 
      • What is health disparities research? 
      • How can informatics and UCSF data science resources be used to conduct health disparities research and address health disparities?

    • Lecture Slides: Overview of Research Data and Resources Available at UCSF

    • Lecture Audio/Video Recording (Access restricted to registered students):  Overview of Research Data and Resources Available at UCSF 

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown


  • Wednesday, January 12, 2022; 11:25 AM - 12:50 PM

    Lecture: Meet Research Analysis Environment (RAE) - The New MyResearch

    Faculty: Rhett Hillary


  • Wednesday, January 19, 2022; 11:25 AM - 12:50 PM

    Lecture:  PatientExploreR
    Faculty: Sam Solodar

  • Wednesday, January 26, 2022; 11:25 AM - 12:50 PM

    Lecture:  COVID-19 Data Sources at UCSF
    Faculty:  Dima Lituiev

    • Lecture Slides: COVID-19 Data Sources at UCSF

    • Lecture Audio/Video Recording (Access restricted to registered students): COVID-19 Data Sources at UCSF

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Drafts of Title, Abstract, Introduction

      Title 

      • Identify the report as a scoping review.

      Authorship 

      • Identify a preliminary author order for your team. This may change by the end of the course and other authors will be added.


      Abstract (at this point this can be rough and conceptual. Update as the paper progresses)

      • Structured summary - Provide a structured summary that includes (as applicable) background, objectives, eligibility criteria, sources of evidence, charting methods, results, and conclusions that relate to the review questions and objectives.

      Introduction

      • Rationale - Describe the rationale for the review in the context of what is already known. Explain why the review questions/objectives lend themselves to a scoping review approach.
      • Objectives - Provide an explicit statement of the questions and objectives being addressed with reference to their key elements (e.g., population or participants, concepts, and context) or other relevant key elements used to conceptualize the review questions and/or objectives.

    • Class Session Recording - Dispararities Impact, Jan 26th, 2022 Media Resource

  • Wednesday, February 2, 2022; 11:25 AM - 12:50 PM

    Lecture: Mapping COVID-19: Health Atlas and Citizen Science Study


    Faculty:  Debby Oh

    • Lecture Slides: 

      Mapping COVID-19:

      Health Atlas

      Citizen Science Study

    • Lecture Audio/Video Recording (Access restricted to registered students): 

      Mapping COVID-19: 

      Health Atlas

      Citizen Science Study

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Methods

      Methods

      • Protocol and registration - Indicate whether a review protocol exists; state if and where it can be accessed (e.g., a Web address); and if available, provide registration information, including the registration number.
      • Eligibility criteria - Specify characteristics of the sources of evidence used as eligibility criteria (e.g., years considered, language, and publication status), and provide a rationale.
      • Information sources* - Describe all information sources in the search (e.g., databases with dates of coverage and contact with authors to identify additional sources), as well as the date the most recent search was executed.
      • Search - Present the full electronic search strategy for at least 1 database, including any limits used, such that it could be repeated.
      • Selection of sources of evidence† - State the process for selecting sources of evidence (i.e., screening and eligibility) included in the scoping review.
      • Data charting process‡ - Describe the methods of charting data from the included sources of evidence (e.g., calibrated forms or forms that have been tested by the team before their use, and whether data charting was done independently or in duplicate) and any processes for obtaining and confirming data from investigators.
      • Data items - List and define all variables for which data were sought and any assumptions and simplifications made.
      • Critical appraisal of individual sources of evidence$ - If done, provide a rationale for conducting a critical appraisal of included sources of evidence; describe the methods used and how this information was used in any data synthesis (if appropriate).
      • Summary measures - Not applicable for scoping reviews.
      • Synthesis of results - Describe the methods of handling and summarizing the data that were charted.
      • Risk of bias across studies - Not applicable for scoping reviews.
      • Additional analyses - Not applicable for scoping reviews.



      * Where sources of evidence (see second footnote) are compiled from, such as bibliographic databases, social media platforms, and Web sites.

      † A more inclusive/heterogeneous term used to account for the different types of evidence or data sources (e.g., quantitative and/or qualitative research, expert opinion, and policy documents) that may be eligible in a scoping review as opposed to only studies. This is not to be confused with information sources (see first footnote).

      ‡ The frameworks by Arksey and O'Malley (6) and Levac and colleagues (7) and the JBI guidance (4, 5) refer to the process of data extraction in a scoping review as data charting.

      $ The process of systematically examining research evidence to assess its validity, results, and relevance before using it to inform a decision. This term is used for items 12 and 19 instead of “risk of bias” (which is more applicable to systematic reviews of interventions) to include and acknowledge the various sources of evidence that may be used in a scoping review (e.g., quantitative and/or qualitative research, expert opinion, and policy documents).


  • Wednesday, February 9, 2022; 11:25 AM - 12:50 PM

    Lecture:  De-Identified Clinical Data Warehouse and the Observational Medical Outcomes Partnership

    Faculty: Eugenia Rutenberg

    • Lecture Slides: De-ID CDW and the OMOP 


    • Lecture Audio/Video Recording (Access restricted to registered students): De-ID CDW and OMOP

       

    • Large Group Discussion (Access restricted to registered students): Brief formal review of lecture followed by question and answer discussion. The recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Results

      Results

      • Selection of sources of evidence - Give numbers of sources of evidence screened, assessed for eligibility, and included in the review, with reasons for exclusions at each stage, ideally using a flow diagram.
      • Characteristics of sources of evidence - For each source of evidence, present characteristics for which data were charted and provide the citations.
      • Critical appraisal within sources of evidence - If done, present data on critical appraisal of included sources of evidence (see item 12 in the methods section of the PRISMA-ScR checklist).
      • Results of individual sources of evidence - For each included source of evidence, present the relevant data that were charted that relate to the review questions and objectives.
      • Synthesis of results - Summarize and/or present the charting results as they relate to the review questions and objectives.
      • Risk of bias across studies - Not applicable for scoping reviews.
      • Additional analyses - Not applicable for scoping reviews.


  • Wednesday, February 16, 2022; 11:25 AM - 12:50 PM

    Lecture: High Performance Computing Environments at UCSF

    Faculty: Ryan Hunt & Henrik Bengtsson

    • Lecture Slides:

      #1 High Performance Computing Environments at UCSF
      #2 High Performance Computing Environments at UCSF

    • Lecture Audio/Video Recording (Access restricted to registered students): 

      High Performance Computing Environments at UCSF
    • Large Group Discussion (Access restricted to registered students): 

      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Discussion, Funding

      Discussion

      • Summary of evidence - Summarize the main results (including an overview of concepts, themes, and types of evidence available), link to the review questions and objectives, and consider the relevance to key groups.
      • Limitations - Discuss the limitations of the scoping review process.
      • Conclusions - Provide a general interpretation of the results with respect to the review questions and objectives, as well as potential implications and/or next steps.

      Funding 

      • Describe sources of funding for the included sources of evidence, as well as sources of funding for the scoping review. Describe the role of the funders of the scoping review. (If you are on a training grant or training funds of any kind you should also note that here)


  • Wednesday, February 23, 2022; 11:25 AM - 12:50 PM

    Lecture:  Information Commons and AI Modeling


    Faculty:     Xinran Liu

    • Lecture Slides:

      Information Commons and AI Modeling

    • Lecture Audio/Video Recording (Access restricted to registered students): Information Commons and AI Modeling


    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Review Scoping reviews of other groups. Identify a journal to submit to and complete formatting for that journal. Try using the Journal/Author Name Estimator https://jane.biosemantics.org/index.php

  • Wednesday, March 2, 2022; 11:25 AM - 12:50 PM

    Lecture:  Electronic Medical Record Search Engine (EMERSE) and Exploring UCSF Clinical Notes


    F    aculty:  Alina Goncharova & Brian Turner

    • Lecture Slides: EMERSE

    • Lecture Audio/Video Recording (Access restricted to registered students): EMERSE


    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown

      Due: Incorporate feedback from reviewers. Make final decision on author order (a good metric is a contribution, but if contributions are equal then alphabetical order is also used). Submit to the journal.

  • Wednesday, March 9, 2022; 11:25 AM - 12:50 PM

    Lecture: Substitutable Medical Applications and Reusable Technologies (SMART) on Fast Healthcare Interoperability Resources (FHIR)

    Faculty:  Eric Meeks

    • Lecture Slides: 

      SMART on FHIR

    • Lecture Audio/Video Recording (Access restricted to registered students): SMART on FHIR


    • Large Group Discussion (Access restricted to registered students):
      Brief formal review of lecture followed by question and answer discussion. Recorded lecture should be viewed prior to this session.

      Zoom: https://ucsf.zoom.us/my/william.brown