Upload and Share Data

Get Permission to Upload Data

The mapMECFS Data Access & Quality Committee (DAQ) approves submission of data to the data platform https://mapmecfs.org. The DAQ will review the mapMECFS Data Submission Request and decide whether to permit the submission. If submissions raise concerns related to privacy and confidentiality, risks to populations or groups, or other concerns, the DAQ will consult with other experts as appropriate. In unusual circumstances, when people are denied approval to submit data, appeals may be sent to the National Institutes of Health (NIH) National Institute of Neurological Disorders and Stroke (NINDS) staff representative to the DAQ.

Steps to Request to Submit Data to mapMECFS by Data Submitters:

  1. Review the capabilities of mapMECFS at https://www.mapmecfs.org/about
  2. Contact the DAQ through mapMECFS (mapmecfs@rti.org) to set up an introductory meeting (preferably 2 months before the desired submission date) to discuss the dataset submission request and resolve technical and other issues.

    The NINDS and mapMECFS staff will discuss with investigators:
    1. dataset submission expectations,
    2. dataset sharing expectations,
    3. supporting materials submission expectations,
    4. dataset access preferences,
    5. technical specifications,
    6. usage of common data elements and globally unique identifiers (GUIDs),
    7. deidentification expectations, and
    8. dataset accuracy as it relates to ME/CFS.
  3. Submit a Dataset Submission Agreement (SA): Read the mapMECFS SA form (below). Submit the SA and Submitter Information and Certifications signed by all necessary parties by emailing a signed copy of this form to mapMECFS (mapmecfs@rti.org). The DAQ may determine that a submitter is exempt from an SA if the data are fully included within a peer-reviewed manuscript.
  4. Dataset SA review: NINDS and mapMECFS staff will review requests to submit datasets to the mapMECFS data platform. Such reviews are generally completed within 10 business days.
  5. Once a submitter has permissions to submit a dataset to mapMECFS, he or she should register for an account on mapMECFS's registration page (https://www.mapmecfs.org/user/register) and follow the steps for data submission as described on the site's About page and the instructions provided during the introductory meeting.
    • Registrants must agree to the mapMECFS DUA and review the site's privacy policy provided on the registration page.

Download a copy of the Data Submission Agreement

How to Upload Data

Once users have obtained approval to submit data, they can upload data files in a variety of file types (TSV, TXT, PDF, etc.) or hyperlinks. To begin uploading data, select the Upload Data icon in the center of the home screen.

When uploading data, you will be taken through the following upload steps. Attempt to include as much information and metadata as possible when creating the dataset, this will help other users on the site understand the data you have uploaded.

Files should be uploaded in the expected format and a dataset should contain the following:

  • One Data File containing sample-level values as columns and molecules as rows.
    Note: An exception is that the data type Demographic, Health, and Survey (DHS) does not support a Data File format. Instead, DHS data are uploaded as a Phenotype File, as shown in the expected format example. The DHS data type is best defined as data collected from study participants that are not derived from biological samples such as blood or saliva.
  • One Phenotype File containing subject-level clinical values, such as case-control status ("Phenotype"), age, sex, any relevant covariates, etc.
  • As many Results Files as needed, including summary statistics for your own analysis on molecules with at least a p-value and adjusted p-value reported.
  • As many Supporting Files as needed, such as:
    • Any relevant documentation describing the study or dataset generation in more detail. Providing additional materials is strongly recommended, as users can better understand the experimental conditions under which the Results Files were generated.
    • A link to existing publication(s)
    • A Data Dictionary File containing information about elements in the Phenotype and/or Data Files. Please refer to the provided Expected Format example, which outlines the suggested column names. Acceptable file extensions for a formatted Data Dictionary include .txt, .tsv, .csv, and .xlsx. A Data Dictionary that does not meet the mapMECFS formatting requirements should still be uploaded as a Supporting Document, but it may not interact with mapMECFS search features.

During upload, Data and Phenotype Files in the expected format will be processed for tagging and summary statistics will be calculated. Results Files will only be processed for tagging when submitted in the expected format. Tagging and calculated summary statistics are not currently available for DHS datasets. More information on summary statistics and tagging can be found within the Process Data section of this manual.

How to Share Data

We encourage researchers to share datasets with other approved mapMECFS site users when the corresponding data is part of a manuscript accepted for publication by making their datasets "public" (viewable to all approved site users). By default, all uploaded datasets will be "private" (only viewable to the uploader and other users registered with the same organization as the uploader).

To change a dataset from private to public, open the dataset you wish to share and select Manage < Current Visibility to Public.

This will notify the mapMECFS site administration of the request, who will review the dataset for breaches of the Data Use Agreement (DUA), non-scientific content, and any personally identifiable information (PII).

Note: It is the uploader's full responsibility to ensure none of these are present, that participant privacy is fully protected, and that sharing is compliant with all other governing policies (e.g., IRB-approved protocols, embargos, etc.). If the specific DUA changes (e.g., retroactive changes in the study’s approved IRB protocols), it is the uploader's responsibility to remove the data or request help from mapMECFS site administrators by emailing mapmecfs@rti.org.

Data uploaded to mapMECFS should never contain PII. Users are recommended to review the U.S. Department of Health and Human Services Safe Harbor Method for more information. In addition, we recommend only including metadata relevant to the study and binning variables (e.g., age 20-30 years), in datasets with few participants (e.g., <30), so that there are always more than three participants in a group no matter how the data is stratified.

mapMECFS does not support the upload of SNP-level genotypes or raw sequencing data; instead, we recommend submitting the data to dbGaP or an alternative database. To make these data findable, users can create a dataset within mapMECFS describing the study with a link to the website containing the raw data and/or study accession IDs.