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DanMobley

DanMobley
Joined Oct 2013
DanMobley
Joined Oct 2013

The National Sleep Research Resource is organizing a meeting with a group of Early Adopters to be held on October 9th, 2015 in Boston, MA, USA. We identify Early Adopters as members of the scientific community who have obtained access to the data on the repository and are employing those data for their scientific research. Also, we would like to welcome any potential new users of the datasets, who may be interested in using NSRR data for their studies. The purpose of this one-day meeting is to bring together a group of “hands on” participants to promote active interaction and collaboration and to provide feedback to improve the value of the NSRR.

Participants in the meeting will have the opportunity to present research in progress using NSRR data, or planned research using NSRR data, report technical bugs, signal anomalies and issues, to highlight tools they want to share, and to interact with the rest of the NSRR community to promote new ideas and identify opportunities for collaboration in the field of sleep research. This is an exciting opportunity to get to know other NSRR users and the NSRR team, and to discuss the latest updates regarding data and tools in the repository. Please also share this invitation with your colleagues, especially trainees and early investigators.

We invite you to complete the application form so we can identify an initial group of individuals who will provide representation of a range of relevant interests and skills. For those who accept the invitation to attend, the NSRR will cover the cost of economy roundtrip airfare to Boston and one night of hotel accommodation. Note that this will be the first of what we hope will be an annual meeting, so even if you do not attend this meeting, we hope you or your colleagues may be interested in future meetings.

Please click on this link to submit your application: https://tryslice.io/survey/national-sleep-research-resource-early-adopters-meeting-10-09-2015

National Sleep Research Resource (NSRR)

Academic User’s Group Meeting and Conference Call Minutes

Monday, March 1, 2014 12pm - 1pm EST

Attendees:

  • Dan Mobley
  • Susan Redline
  • Tricia Tiu

Via Conference Call:

  • C. Johnson*
  • D. Gottlieb*
  • J. Wilson*
  • P. Peppard*
  • S. Warby*
  • S. Surovec
  • A. Goldberg
  • R. Mueller
  • J. Cai

Response to Feedback from Previous Call: S. Redline gave update on the response to feedback from previous AUG call (01/31).

  • Created support@sleepdata.org email address to provide contact information for users with questions. It is made prominent on page.
  • FAQs and tutorials pages were created. They are currently under SHHS documentation. There are four tutorials in place
    • 1. How to browse through documentation
    • 2. How to go through DAUA process
    • 3. How to download EDFs
    • 4. How to request file access
  • Linked variables to form pdfs. Variables can be filtered to show all variables collected for that specific form.
  • Added documentation for CHAT and HeartBeat studies.

Response to Feedback w/ S. Warby and P. Peppard: In response to feedback from AUG members, S. Warby and P. Peppard, priorities have been focused to providing thorough data dictionaries to allow mapping within cohorts, rather than across cohorts

Updates to Data Resource: SleepData.org will be released to the public on Tuesday, April 1. All SHHS studies will be made available, once users are granted access. SHHS data is linked to BioLINCC using a common ID. CHAT data will be released and made available ~July 1.

New ABOUT page: About page was created for NSRR members and AUG members to introduce users to our team.

New Tools: The purpose of provided tools is to work tightly with data provided in data set. Tools are designed to do ‘pre-processing’ of dataset for users.

  • An EDF (European Data Format) is a somewhat standardized file format that allows the visualization of signals from PSG studies, XMLs contain the scored annotations of the PSG studies. Both can be used separately or overlaid for a more robust analysis.
  • EDF Editor and Translator Tool – Java-based tool de-identifies and normalizes signals by editing EDF files
  • EDF Viewer Tool – Allows users to open and view an EDF file and scroll through signals.
  • Block EDF Loader – Allows users to load an EDF into MATLAB and to access a specific signal present in the EDF file

DAUA Process and Updates: DAUA process has been established. All users must submit a DAUA, along with IRB review/approval, in order to obtain access to the data sets. Each data set will require a separate DAUA from each user. The DAUA grants the user approval for 3-years of access to the data set or until the expiration date, as outlined in the user’s IRB approval.

  • We are looking to streamline DAUA process and try to reduce barriers to the access of datasets while staying within the limits of the different cohort’s and our own institution’s (BWH-Partners) requirements. Since the data is completely de-identified, it can be argued that research using that data would not be considered “human research” and not require IRB review and approval. For now, we will keep DAUA process in place; S. Redline will begin working with cohort representatives to understand what each steering committee and IRB truly requires.
  • S. Redline brought up question of whether trainees or use of data for educational purposes (such as scoring exercises) would be covered under IRB. Should trainees be granted access to dataset without IRB approval unless they plan on publishing papers using data? Would an attestation be more appropriate?

Other enhancements planned: We plan on providing a forum for users to meet other researchers from the community. Strength of forums is driven by users, not by the format of the forum.

Action Items:

  • AUG members review their biography on ABOUT page (https://sleepdata.org/about/aug). Confirm whether information is correct. Send bios to Tricia Tiu (ttiu@partners.org) if you haven’t done so already.
  • AUG members review documentation and provide feedback on anything that is lacking or needs to be emphasized.
  • AUG members will need to go through DAUA process to get access to data. Members do not need to provide IRB approval or review, unless they intend on using data to publish papers.
  • Would members be interested in a get-together at Sleep meeting at end of May?
  • We plan on hosting our first face-to-face meeting in the next 6-9 months, depending on scheduling and availability of key members.

National Sleep Research Resource (NSRR)

Academic User’s Group Meeting and Conference Call Minutes

January 31, 2014 3:00 p.m. EST

NSRR Participants

  • Susan Redline
  • Remo Mueller
  • Michael Rueschman
  • Susan Surovec
  • Daniel Mobley
  • Ary Goldberger

AUG Members

  • Florian Chapotot
  • Nalaka Gooneratne
  • Daniel Gottlieb
  • Craig Johnson
  • Paul Peppard
  • Katie Stone
  • Simon Warby
  • James Wilson
  1. Introduction/Welcome to the AUG Susan R. opened the meeting and provided a brief introduction of NSRR staff members from Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center, and Case Western Reserve University. A brief introduction of the AUG members was then provided.

  2. NSRR Overview Susan R. provided an overview of the NSRR grant main goal, and discussed collaboration with BioLincc and possible future collaboration with dbGaP. Funding for NSRR is via a 5 year NIH/NHLBI grant with support from Brigham and Women’s Hospital (BWH) in years 6 through 10. The NSRR Aims were described (summarized below), and an NSRR Organizational chart was presented with an explanation of the working groups/teams.

    • a. Aim 1—Sleep-Arch: Electronic data library containing raw signals, scored annotation files, sleep summary statistics curated from 15 large-scale research studies of adults and children. Also will include time and frequency domain analyses for ECG and EEG signals from the PSGs, and will link PSGs to covariate data and spectral analysis results.
    • b. Aim 2—Sleep-Terms: Create a standardized infrastructure to support terminology across the data library with mappings of terms and covariate data to a common terminology.
    • c. Aim 3—Sleep-Port: A web-based portal to access, search and visualize the data library using a cloud-based platform. This resource is currently hosted at BWH in Boston but will eventually be cloud-based.
    • d. Aim 4—Sleep Tools: Provide a suite of data curation, data integration and signal processing tools to facilitate offline analysis and discovery of associations among physiological systems and clinical outcomes by investigators. The plan is to provide tools to normalize/standardize EDF files and allow viewing of physiological signals collected using diverse proprietary platforms, and tools to conduct offline spectral analysis as well as advanced processing of ECG, EEG, and breathing signals.
    • e. Aim 5—Support the research community.
  3. Purpose of the AUG Susan R.—Academic User Governing Committee is comprised of key stakeholders who are representatives of major participating study groups, community users, and technical experts. The AUG will meet bi-monthly via conference call and 1 to 2 times annually in person. The AUG will develop governance policies, provide input into usability, accelerate the dissemination of tools, help prioritize tasks, provide feedback on web-based user guides and webinars, and create a dynamic user community.

  4. Unveiling of sleepdata.org Remo M. created a survey requesting feedback from AUG members after the meeting and explained the 3 components of sleepdata.org: Explore datasets, download data, analyze data.

    • a. Sleepdata.org site demo: Remo provided a demo of the site that included review of uploaded SHHS documentation, variable searching and site navigation, downloading EDF data as single files or full set of files using WGet, demo of annotation files and description of how to visualize annotations, review of posted forms used during study collection, and an overview of tutorials.
    • b. Sleepdata.org Tools and Resources: Remo gave an overview of the “Tools” page and used the Block EDF Loader tool as an example of a tool hosted on the site. A description of the PhysioMIMI tools link was provided as an example of a resource hosted on an external site. Dan G. questioned if the ability to view and process physiological signals in the cloud would be available versus having to download the files to a local machine. Ary G. stated this could be possible in the future, but deferred to Remo who explained the current plan is to provide small tools for download that can be extended by the user or a programmer. Susan R. suggested, as a topic for a future call, the group consider what functionality they would want if a resource existed to allow access to data easily.
  5. Regulatory Issues Susan R. explained that NSRR is trying to be as congruent as possible with BioLincc and to closely collaborate with that group. BioLincc has agreed to provide a link on their site to sleepdata.org when the BioLincc data repository contains data from research participants who also have PSG data residing in the NSRR. NSRR has agreed to do the same. In the future, NSRR hopes to form a similar relationship with dbGaP. Susan R. also discussed the need for a Data Use Agreement (DUA) and IRB review at sites wishing access to NSRR data. Susan R. will work with cohorts to ensure Steering Committees are comfortable with the data that is being shared.

  6. Questions from the AUG

    • a. Simon W. requested a high level overview of the Sleep-Terms group and asked about how the group plans to deal with variables, especially for longitudinal data. Susan R. suggested a 1 hour webinar devoted to this topic. A high-level overview of the canonical data dictionary was provided. Remo described the data dictionary foundation underlying the current process. The Sleep-Terms group is working on a mapping matrix.
    • b. Paul P. hopes to make the Wisconsin cohort data available and ask for key contact information. A contact list will be provided, and Susan R. suggested keeping contact information online as well as possibly using the Wisconsin data as as a use case for how to bring a cohort or dataset online in NSRR.

Action items:

  • Distribute slide presentation used for meeting in PDF format (Dan M.)
  • Create a list of key NSRR contacts for AUG (Dan M., Remo M.)
  • Arrange future calls, when appropriate, to discuss
    • 1) desired functionality of a resource that allows easy access to data and
    • 2) canonical data dictionary and how variables are handled.