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  1. A short phrase describing your study, and a study abbreviation 

    • We use the abbreviation to annotate all content associated with the study. Examples:

      • The Mount Sinai Brain Bank (MSBB) study

      • The Mayo RNAseq Study (MayoRNAseq)

  2. The name and contact info of a team liaison

    • This person will be my main contact for the team, and will triage tasks. This does not have to be the person responsible for data upload, and ideally should not be the PI

    • A list of the people on your team you want attributed in the portal as having contributed to your grant(s). 

      1. We do this by linking to people’s Synapse profile (The AD Knowledge Portal’s data management system). To create a Synapse profile see here: https://www.synapse.org/#!RegisterAccount:0

      2. Ideally Synapse profiles should include full name, a photo, and affiliated institution. People can also include a bio (or link to one) if they so wish.Those with a profile containing photo, are featured on the front page of the Portal (all members are listed under Explore - People irrespective of profile completeness)

    • In addition to the AD Knowledge Portal, we manage a private collaboration space within the Synapse platform. This space has limited access to members of the funded AD Knowledge Portal Programs and is a place for the distribution of meeting materials, information about working groups etc. Please indicate which of your team members you would like to have access to the AD consortia private space/resources. We will add them to a Synapse team that provides access

  3. Write an acknowledgement acknowledgment statement for your data. 

    • Users of the data will be requested to use this statement in publications.

    • Example:  "These data were generated by Kristen Brennand, a New York Stem Cell Foundation - Robertson Investigator. This work was supported by the Brain and Behavior Research Foundation, NIH grant R01 MH101454 and the New York Stem Cell Foundation."

    • The template for writing the acknowledgement acknowledgment statement is here: https://www.synapse.org/#!Synapse:syn25014532

    • The form to submit the completed statement is here: https://www.synapse.org/#!Synapse:syn25051271

  4. If you have a manuscript being prepared, please fill out this form detailing the data used in the manuscript so we can begin setting up the infrastructore infrastructure for the data: https://docs.google.com/forms/d/e/1FAIpQLSeQjHkj72iZuwMzwhmXXwi7fhK4d57skDHwrjC5Kaldr4DHVw/viewform

    1. The NIA requests that AD Knowledge Portal funded partners include a specific data availability statement in manuscripts based onuse of data from the portal:

      1. <data, analysis output, tools (describe content)> are available via the AD Knowledge Portal (https://adknowledgeportal.org/). The AD Knowledge Portal is a platform for accessing data, analyses, and tools generated by the Accelerating Medicines Partnership (AMP-AD) Target Discovery Program and other National Institute on Aging (NIA)-supported programs to enable open-science practices and accelerate translational learning. The data, analyses and tools are shared early in the research cycle without a publication embargo on secondary use. Data is available for general research use according to the following requirements for data access and data attribution (https://adknowledgeportal.org/DataAccess/Instructions).
        For access to content described in this manuscript see: <manuscript landing page DOI>

      2. The AD-DCC will provide you with a doi to use in the manuscript as a data reference.

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  • Study description

  • Assay description

  • Acknowledgement Acknowledgment Statement

Please submit these documents through this form. https://www.synapse.org/#!Synapse:syn25051271

  • Links to the templates for writing these are at the top of the form

  • You don't need to submit everything at once, and you can submit as many times as you want

  • If there are other team members that you want to be linked to the grant, have them create a Synapse account and submit their Synapse name through the form. I'll link them to the grant.

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  1. You fill out your templates and manifest and validate them in the dccvalidator

  2. Continue to validate your files until there are no more failures (the red section)

    1. This often is a round of collaboration between you, me and our data curator - the validator can be somewhat cryptic about what it's throwing failures about, so email me if you run into problems or questions.

    2. If you want to find any controlled values, for example, a platform, you can use our data dictionary - the main search box is in the upper right-hand corner: https://www.synapse.org/#!Synapse:syn20729790

  3. Once the files have passed validation, email me. Our data curator will do some manual curation, and then I'll give you the file location and permission to start the data and metadata upload.

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Please let me know if you have any questions!

4. Uploading Data to Synapse

SUBJECT: MODEL-AD - Study - Uploading Data

Here is an overview of the expected data contributions and timelines for your study. Please let me know if you have questions.

Study Information

Program: MODEL-AD

Grant: U54AG123456 

Study: Site_Study

Abbreviation: Study_Abbrev

Staging: URL_here

Transfer: Data will be ready for upload during January 2022

Metadata

Data

Upload

The web interface works well for quickly transferring a few files, but the Synapse client should be used for uploading files in bulk. 

Documentation