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Uploading Animal Model Documentation

This article will teach you how to share your MODEL-AD animal models with the AD Knowledge Portal’s Data Coordination Center (AD-DCC) at Sage Bionetworks.

MODEL-AD Tools Survey

MODEL-AD teams should inform the AD-DCC about new models by completing the MODEL-AD Tools survey. The descriptive content entered into the survey will be used to populate the corresponding Experimental Tool cards listed in This page describes the procedure for how MODEL-AD teams should submit mouse models to the DCC. The mouse models will be posted on the experimental tools page on the AD Knowledge Portal.

Each model should include the key details listed below and a brief study description of how the animals were created. The model details should match the information on the Jackson labs stock pages, and any discrepancies will need to be resolved.

Model Information to include

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Step 1: Submit Mouse Model details

Please provide information about the mouse model in this MODEL-AD Tools survey. The strain information should match that on the JAX stock page.

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• Email address of the person submitting the survey

• Grant number

• Species

• Model Common Namesystem name (see names in the AD Metadata Dictionary)

• Model URL (link to the Jackson Lab model, eg, to Jax stock page (ex: https://www.jax.org/strain/123456031988)

• Report card URL (link to the AlzForum research model (ex: https://www.alzforum.org/research-models/3xtg)

• Model description (<500 characters)Targeted

• GenesList of genes the model is targeting

• Background strain (eg, C57BL/6J)

• Type (LOAD – Late Onset Alzheimer’s Disease, FAD – Familial Alzheimer’s Disease)

Add Model to Synapse

Create Model Entity in Synapse

• At the bottom of the survey, you can upload a PDF of the Mouse Model Report. The AD-DCC will add it to the Mouse Model Reports in Synapse.

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Step 2: Model added to the Portal

The DCC creates a new entity in Synapse’s Experimental Tools for your model. The Synapse entity will be named after the Model Common System Name and will . This entity will be annotated with the information provided, including a link to the Jax lab stock page.

1. Navigate to AD Knowledge Portal’s Experimental Tools page

2. Click Folder Tools > Add New Folder

3. Name the folder with the Model Common Name

4. Add a URL to the Jackson labs strain (eg, https://www.jax.org/strain/123456)

Annotate Model

The AD-DCC will then annotate the model entity further with the content provided in the survey.

1. Navigate to the Experimental Tools file view

2. Download the Experimental Tool

   1. Click Download Options > Export Table

   2. Click Download as CSV

3. Add annotations to CSV file using a text editor or spreadsheet software

4. Upload your revised CSV to the entity view to populate annotations

Link to Experimental Study

The AD-DCC will link all of the data in Synapse that uses the model. This is a Synapse file view that includes a query for all data associated with the model and will not be limited to individual studies.

1. Navigate to …

Create and share Model release notes

Sage DCC writes release notes to inform the community that a new model is available. The release notes must link to the Experimental Model card in the AD Knowledge portal.

Past release notes are available in this document.

MODEL-AD teams provide mouse model reports

MODEL-AD teams must provide a mouse model report in PDF format. Example reports for MODEL-AD are available here in Synapse.

Sage DCC uploads mouse model report

The Sage DCC will upload the mouse model report PDF into JAX stock page, and a list of studies that include data from the model.

The DCC will add the PDF report to the Mouse Model Reports in Synapse.

Sage sets necessary sharing permissions

Since the mouse model reports do not include sensitive information or PII/PHI, they are eligible for anonymous viewing and download permissions in Synapse. The Sage Governance team is responsible for enabling sharing permissions for each file in Synapse.

To set permissions the DCC curator must:

• Create a Jira ticket and assign to Director.

• The director will assign Jira ticket to the Sage Governance team.

• Governance will set permissions as needed at the file level.

Sage DCC updates file view with link to model report

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Step 3: Community Update

The DCC informs the community when a new model is available on the Portal in the AD Knowledge Portal News. See past Public Data Release Notes.