The AD Knowledge Portal supports Alzheimer's disease researchers in fulfilling journal and funder requirements to make published data, code, and analysis results Findable, Accessible, Interoperable, and Reusable (FAIR). This page describes how to use a Synapse Dataset to group content hosted in the AD Knowledge Portal, and link that Dataset to your manuscript's Data Availability Statement through a persistent identifier (DOI).
For guidance on whether you need a Publication Dataset at all, and the required Data Availability Statement format, see Acknowledge Data.
1. Contact us early.
When planning a manuscript based on data hosted in the Portal, submit a Request a DOI for Publication Service Desk request as early as possible in the process.
Tell us:
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The Synapse username(s) of anyone who should have edit permission on your Dataset (e.g., manuscript coauthors, collaborators).
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Whether you have analysis files related to your manuscript that aren't already in the Portal and that you'd like to include.
2. Upload analysis files (if applicable).
Upload any additional files and analysis outputs associated with your manuscript to a designated Analysis Folder which will be provided to you by a member our team. You may use the Synapse web UI to do so, or you may upload files in bulk with a programmatic client. Annotating analysis files is optional but recommended.
Once uploaded, we'll verify your files don't contain sensitive data and make them public so they can be included in your Dataset.
Analysis Files may include:
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Contextual files associated with your manuscript which are available to the public without signing a Data Use Agreement of any kind
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Summary or aggregate-level data (e.g., differential expression results, summary statistics, model parameters)
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Code or processing scripts
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Supplementary tables, protocols, or diagrams that don't contain identifying or sensitive information
Manuscript-related analysis files can only be uploaded if they meet open-access governance criteria.
Sharing Controlled Access data (e.g. individual-level data such as identifiers, sequence data, gene counts, or clinical data) related to your publication via upload to an Analysis Folder will result in a data privacy violation.
3. Open a separate ticket to share reusable Analytical Outputs (if applicable).
To share reusable Analytical Outputs through the AD Knowledge Portal, particularly those which must be subject to controlled-access data governance, you’ll need to open a separate Service Desk ticket using the Add Analytical Outputs request type. This related process is outlined in our Help Doc on Contributing Analysis and Results Data.
Analysis Folder Content vs. Analytical Output: What’s the difference?
Differentiating between analytical files which can be uploaded to an Analysis Folder vs. those which should be shared by opening a ticket to Add Analytical Outputs can be confusing! Refer to the below table for a breakdown of the two pathways for sharing results associated with your manuscript.
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Analysis Folder Files |
Analytical Outputs (Separate Ticket) |
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Primary Scope & Purpose |
Contextual supplementary files specifically tied to the analysis performed, useful for understanding a specific manuscript. |
Standalone, reusable analytical outputs intended for other portal users to generate new insights. |
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Portal Integration |
Not surfaced on the AD Knowledge Portal for other users. Accessible only via a Synapse Dataset DOI. |
Curated and shared broadly with other portal users directly via the portal interface. |
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Data Governance & Agreements |
Must meet open-access governance criteria (publicly accessible). |
May be subject to controlled-access data governance. A data transfer agreement is required before upload. Curation efforts must be funded. |
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Allowed Content |
Summary/aggregate data (e.g., differential expression, summary statistics), code/scripts, supplementary tables, or protocols. |
Individual-level human data (e.g., individual clinical measurements, genomic/sequence data, gene counts) or broadly applicable analytical resources. |
4. Add items to your Dataset
A blank, empty Dataset will be provided to you by a member of our team. Go to your Dataset and add items. You can add any files you have access to from anywhere in Synapse, and specify the exact file version used in your analysis if a file has multiple versions.
For AD Knowledge Portal Datasets, include:
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All raw or processed data files used in the analysis
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The individual, biospecimen, and relevant assay metadata files from all Portal studies included in your Dataset
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Any analysis, results, or additional files from your Manuscript-Related Analysis folder
5. Customize your Dataset wiki
Go to Dataset Tools → Edit Dataset Wiki to add the following elements:
Required:
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Manuscript or journal article title
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Full author list for the manuscript
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Publication or pre-print URL
Update the link to your publication over time to include both the pre-print and the peer-reviewed journal article once published; list all publications that reference this Dataset.
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The Synapse username of a "Dataset contact" — this should be the same person listed as the primary contact for the manuscript (type
@and search for the name) -
The acknowledgement statement(s) from each AD Knowledge Portal study referenced in your Dataset — see Acknowledge Data. You should also include your own manuscript-specific acknowledgement statement in addition to these.
Optional: You are encouraged to include anything else that helps contextualize your dataset or analysis (see Synapse Wikis for adding links, tables, and images)
6. Customize your Dataset schema
Edit the Dataset schema to customize which columns are displayed. A good default is to select "Add Existing Annotations," which includes all annotations we apply to files in the Portal.
7. Create a stable Dataset version
Once your wiki details and Dataset items are finalized, create a stable version with an informative comment — e.g., "Dataset for manuscript submission April 2026" or "Finalized analysis for Smith et al. 2026 publication." If you need to make further changes later, edit the draft version and create a new stable version with a new comment.
Important: you MUST manually version your Dataset! Unlike files, which are automatically versioned anytime the file is updated, saving changes to a Dataset will not automatically create a new version.
8. Mint your DOI
From your stable version, go to Dataset Tools → Create a DOI and mint the DOI. DOI metadata becomes public, so be sure to enter manuscript-relevant information.
Once minted, add the DOI to your manuscript's Data Availability Statement — see Acknowledge Data for the required format.
Important: Don't stop at your Draft DOI! Early in this process (for example, while preparing a pre-print), you may be provided with a preliminary DOI pointing to your Draft, unversioned Dataset. This DOI is not final. Before your manuscript's final publication, you must return to your Dataset, create a stable version, and mint a new versioned DOI. Then, update your Data Availability Statement to reference the versioned DOI.