FAQ

For specific term definitions, see our Glossary.

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Portal Content

What data and tools are available in the portal?

The portal provides data from a variety of human and model systems, including clinical assessments, animal behavior, and genomic analysis. Much of the data is from post-mortem brain tissue, but there is also data from living cohorts. The data provided depends on the assay and study, but typically includes raw and processed data. The portal also provides access to computational and experimental tools for general use by the research community.

Data Access

Why should I be certified on Synapse, and what does that involve?

If you’ll be uploading data to your project, you must become certified on Synapse before doing so. You also must be certified in order to request access to specific Controlled Access data. Certification requires the completion of a short quiz, which ensures you have awareness of privacy and security issues associated with using a platform that stores human subjects research data. Learn more about the different levels of Synapse users, and what you are able to do at each level, here.

How can additional people on my team get access to Controlled data?

Find full instructions here.

My access request was approved, but I still cannot download the data. Why is this?

Make sure you have accepted all terms and conditions, and that you are logged in with the account that was approved. Find more information on data access here.

My access request was denied. Why?

Check for an email detailing the reason for the request rejection. Some common issues are: the Synapse usernames on the DUC and the request do not match; the DUC does not have a signing official or the uploaded document is missing a page; the project lead and/or institution field is not complete; or the intended data use (IDU) statement needs more detail (IDUs should be 1-3 paragraphs and address the following points: What do you want to do? Why are you doing it? How do you want to do it?).

Someone else originally added me to their Data Use Certificate. How can I renew my access?

The primary requestor must be the person to renew the request.

I have moved to a new institution. Can I keep my current data access?

No, the data access request and associated DUC only cover individuals from the same institution as the signing official and you must update your access request if you move institutions. You will need to update your request so that reflects your current institution (the affiliation field) and submit a new DUC signed by a signing official at your new institution.

My access has expired, what do I do?

If you need continued access to the data, you will need to resubmit a new access request. If you are closing out access, you need to delete all copies of the data your team has downloaded. The terms of use also require that you provide a brief summary of what you accomplished with the data.

Why are ages over 90 censored in the Covariate or Clinical files?

Including ages over 89 changes the level of protection needed for the Data as per HIPAA regulations.

About Data and Metadata

What is metadata and why is it important?

Metadata provides information about the data in the portal. Metadata can be associated with individual subjects and/or with files.

For more information, including how to annotate your own data with metadata, see About Metadata.

How can I find the metadata associated with a study?

There are two main ways to access the metadata files associated with a study in the AD Knowledge Portal:

Click Explore → Studies → find and click on the Study of interest to access the corresponding Study Details page → click on the Study Data tab → navigate to the Study Metadata section, which shows a table of all the metadata files for that study
Click Explore → Data → use the Study section of the Filter By toolbar at the left to select your study of interest → use the Data Subtype section to select metadata

For a more detailed breakdown of these steps, please see How to find and download metadata files.

Why are there multiple metadata files for a study?

There are three primary types of metadata files, which provide information about 1) the individual (e.g., human subject, animal, or cell line), 2) the specimens (“biospecimens”) used in assays (e.g., information about brain samples from an individual subject), and 3) assays and assessment variables (e.g., details about RNAseq library preparation or proteomics sample preparation). Dividing the information in separate files decreases the possibility of copy errors and increases the efficiency of adding information about new individuals, biospecimens, and assay details. It also allows you to gather only the information you need for your desired dataset.

For more information, including how to annotate your own data with metadata, see About Metadata.

How do I combine metadata files to get the full dataset?

In studies where data has been generated from a specimen taken from an individual, the biospecimen metadata file acts as the link between the individual metadata file and assay metadata file(s). These can be linked together by joining the individual and assay metadata files to the biospecimen using the individualID and specimenID, respectively. In studies where data has been generated based on an assessment, the datafile and assay metadata can be directly linked to the individual metadata file through the individualID. For a more detailed breakdown of these steps, please see our Use Case #3: Accessing and Joining Metadata Files With Data.

When accessing data, how can I determine if it’s raw or processed?

This is a specific annotation assigned to data, so you can filter for it using the filtering tools on any of the Explore pages. Use the Data Subtype to identify raw data (e.g. fastq files) or processed files (e.g. gene count matrices) or the File Type filter to help identify raw or processed files.

How is diagnosis determined for the data?

Alzheimer’s disease can be diagnosed in many ways, and this diversity is reflected in differences in diagnostic criteria by different research groups. The postmortem data in the portal is in the process of being annotated with "Alzheimer's disease" or "Control" based on CERAD and Braak scores. Explore individual studies for information.

How can I find summaries of the methods used to generate data?

Documentation and methods are located on each Study Details page. Click Explore → Studies → find and click on the Study of interest to access the corresponding Study Details page. Some studies have additional study documentation and detailed protocols provided as pdf files. These have been annotated with metadataType=protocol.

Publishing on AD Knowledge Portal Data

Is there an embargo on publishing results from use of any of this data?

Data from the Portal is available for general research use, with no embargo on publishing results.

Human individual-level data is Controlled Access. What this means is that you can not share individual-level data in any form (raw, processed, derived) outside the AD Knowledge Portal.

How can I properly acknowledge AD Knowledge Portal datasets in a manuscript?

The data available in the Portal would not be possible without the participation of research volunteers and the contribution of data by collaborating researchers. Any publications that result from your use of the data must include appropriate Acknowledgement Statements to abide by community guidelines.

Where can I share information about my upcoming publications that used AD Knowledge Portal data?

If you'd like to provide updates on datasets or share recent publications, submit content for the quarterly public newsletter by contact us through the Forum.

Additional Help

How can I receive updates on data releases and new portal features?

The AD Knowledge Portal publishes a quarterly newsletter that provides updates on data releases and new portal features; view all previous newsletters and sign up to receive the AD Knowledge Portal quarterly Newsletter .

How do I know when new data has become available?

New data and updates to previously released content are documented through regular Data Releases. Announcements about data releases are also made through the Discussion forum and Twitter. Request to join the AMP-AD_DataReleaseUpdates team to receive these updates directly.

Can I share my own data through the AD Knowledge Portal?

If you have data, analyses, or tools that may benefit Alzheimer’s disease research you can apply to become a community contributor and have your resources hosted in the portal. Learn more about how to contribute.

How can I provide feedback on the portal and/or this help site?

For more information or to offer general feedback on the AD Knowledge Portal or on this help site contact us through the Forum.