Submitting MODEL-AD Experimental Tools

Getting Started

To upload data, you’ll need to do the following:

1. Create a Synapse account.

2. Complete a brief quiz to become a Synapse certified user.

3. Become a member of the MODEL-AD Data Upload team.

If you have questions about any of these steps, or to request access to the MODEL-AD Data Upload team, please contact Sage’s AMP-AD Administration team.

Uploading Model Documentation

Mouse Model Description

This article will teach you how to submit new rodent models to the Data Coordination Center (DCC) at Sage Bionetworks. To start, MODEL-AD teams must inform the DCC about new models by submitting a complete and accurate description via the MODEL-AD Tools survey. The content entered into the survey will be used to populate the corresponding Experimental Tool card in the AD Knowledge Portal. Each mouse model should be accompanied by a brief study description that includes the species, genetic background, a link to the Jax Datasheet (if available) or a description of how the animals were created.

Metadata Key Variables

Mouse models must include the information listed below. The model information should match that on the Jackson labs stock pages, and any discrepancies will need to be resolved. If you have any questions, please contact the DCC before submitting.

• Email address for contact person

• Grant number

• Species

• Model Common Name

• Model URL (link to the stock number in the Jackson Lab database)

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

• Model description (<500 characters)

• Targeted Genes

• Background strain

• Type (Late Onset AD, Familial AD)

Create Model Entity in Experimental Tools

The Sage DCC will create a new entity in the AD Knowledge Portal’s Experimental Tools file view. The new entity will be named after the Model Common Name and will include a link to the corresponding Jackson labs Model URL webpage.

1. Navigate to AD Knowledge Portal’s (File > Portal > ExperimentalTools) 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

Sage DCC adds annotations to folders using the using the file view.

1. Navigate to the AD Knowledge Portal - backend > Portal - Experimental Tools

2. Download the Portal - Experimental Tools

   1. Click Download Options > Export Table

   2. Click Download as CSV

3. Add annotations to file

4. Upload data to entity view to populate annotations

Link to Experimental Study

Sage DCC enters link to study with the data available for the model.

• Note: Although not implemented yet, there has been a discussion about linking to a query of all data from the model instead of individual studies.

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 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

Sage DCC updates file view with a link to the mouse model report in the [Portal - Experimental Tools](https://www.synapse.org/#!Synapse: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 )