Documentation for how to provide information about new strains

This article describes the process for how the MODEL-AD teams submit new strain information. This information will be posted as in experimental tools on the AD Knowledge Portal’s Data Coordination Center (AD-DCC).

Step 1: MODEL-AD submits information about the new strain

Strain Information to include

Each strain should include the key details listed below. The model details should match the information on the Jax strain webpage, and any discrepancies will need to be resolved.

• Email address for the person submitting the survey

• MODEL-AD Grant number

• Species

• Model Common Name as used in the strain list on the MODEL-AD Strain Table

• Model URL (link Jax strain page – eg, ex: https://www.jax.org/strain/031988 )

• Report card URL (link AlzForum modelstrain, if available – ex: https://www.alzforum.org/research-models/3xtg )

• Model description (<500 characters)Targeted Genes

• A list of genes the model is targeting

• Background strain

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

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MODEL-AD teams provide mouse model reports

MODEL-AD teams should provide a mouse model report in PDF format.

The MODEL-AD data liaison should provide the AD-DCC with this report somehow and at some interval….

Test and see if Google forms allows for attachments. We could capture the report at the same time.

The Sage DCC will add the mouse model report into the Mouse Model Reports in Synapse.

Step 2: AD-DCC Adds new strain to the AD Knowledge Portal

Create Model Entity in Synapse

The AD-DCC will create creates a new file entity in Synapse’s Experimental Tools for your modelthe strain. The Synapse entity will be is named after the Model Common Name and will link to the Jax lab stock strain 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 annotates 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 annotationsAnnotate new strains by editing the query results or by downloading a CSV

Link to Experimental Tool

The AD-DCC create creates a link to any study that includes data from the model.

This is a Synapse file view that includes a query for all data associated with the model and is not limited to individual studies.

MODEL-AD teams provide mouse model reports

MODEL-AD teams should provide a mouse model report in PDF format.

The MODEL-AD data liaison should provide the AD-DCC with this report somehow and at some interval….

Test and see if Google forms allows for attachments. We could capture the report at the same time.

The Sage DCC will add the mouse model report into the Mouse Model Reports in Synapse.

strain.

AD-DCC 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:

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Create a Jira ticket and assign to Director.

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Sage

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Governance will set permissions as needed at the file level.

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DCC updates file view with link to model report

Sage DCC updates file view with a link to the mouse model report in the Experimental Tools

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Step 3: Creating release notes and advertising new strains

The AD-DCC writes release notes to inform the community that when a new model strain is available. The release notes will are posted in News stories and link to the Experimental Model card experimental tool in the AD Knowledge portal. Additionally,

Past release notes are available in this document.

Zoe posts release notes in news section of portal.

When a new model available should create strain is available the AD-DCC will write a feature story about model in newsletter (**Discuss this option w/ MODEL-AD teams**)News stories