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Provide 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
This page describes the procedure for how MODEL-AD teams should provide the AD-DCC with information 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 submit mouse models to the DCC. The mouse models will be posted on the experimental tools page on the AD Knowledge Portal.
Model Information to include
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 number, and any discrepancies will need to be resolved.
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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 Name and will link to the Jax lab stock page.
Navigate to AD Knowledge Portal’s Experimental Tools page
Click Folder Tools > Add New Folder
Name the folder with the Model Common Name
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.
Navigate to the Experimental Tools file view
Download the Experimental ToolClick Download Options > Export TableClick Download as CSV
Add annotations to CSV file using a text editor or spreadsheet softwareUpload your revised CSV to the entity view to populate annotations
Link to Experimental Tool
The AD-DCC create 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 System Name. This entity will be annotated with the information provided, including a link to the 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.
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:
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 Experimental Tools
Create and share Model release notes
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Step 3: Community Update
The DCC informs the community when a new model is available . The release notes will link to the Experimental Model card on the Portal in the AD Knowledge portal.
Past release notes are available in this document.
Zoe posts release notes in news section of portal.
When new model available should create a feature story about model in newsletter (**Discuss this option w/ MODEL-AD teams**)
News stories Portal News. See past Public Data Release Notes.