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This page describes the procedure for how MODEL-AD
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This article will teach you how to submit new rodent teams should submit mouse 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 mouse models will be posted on the experimental tools page on the AD Knowledge Portal.
Metadata Key Variables
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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 Jackson labs stock pages, and any discrepancies will need to be resolved. If you have any questions, please contact the DCC before submitting.JAX stock page.
Email address for contact personof the person submitting the survey
Grant number
Species
Model Common Namesystem name (see names in the AD Metadata Dictionary)
Model URL (link to the stock number in the Jackson Lab databaseJax stock page (ex: https://www.jax.org/strain/031988)
Report card URL (link to the research model in ALZFORUM 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 ADAlzheimer’s Disease, FAD – 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.
Navigate to AD Knowledge Portal’s (File > Portal > ExperimentalTools) 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
Sage DCC adds annotations to folders using the using the file view.
Navigate to the AD Knowledge Portal - backend > Portal - Experimental Tools
Download the Portal - Experimental Tools
Click Download Options > Export Table
Click Download as CSV
Add annotations to file
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 should provide a mouse model report in PDF format. See example here [add link]
Sage DCC will mouse model card in Synapse to this mouse model report.
For this information to be visible publicly, the DCC team must:
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Create Jira ticket and assign to Director.
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Once approved, the Jira ticket will be assigned to the Sage governance team who will set permissions as needed. The permissions for each file must be set at the file level rather than folder level.
Sage team links mouse model report
Sage DCC uploads reports to [MouseModelReports](https://www.synapse.org/#!Synapse:syn25474060 )
Sage DCC requests necessary permissions
Sage DCC requests that the PDF model report is permitted to be publicly available in Sage without restriction. [Enable Anonymous Download of Synapse Data](How to Enable Anonymous Download of Synapse Data )
Sage DCC updates file view with link to model report
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Alzheimer’s Disease)
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 named after the Model 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. 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.
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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.