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Getting Started
To upload data, you’ll need to do the following:
Complete a brief quiz to become a Synapse certified user.
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 Study Documentation
Study Description
Each study 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.
Assay Description
Each assay should be accompanied by a short description that includes specimen processing, data generation, and data processing, as applicable -- something akin to the Materials and Methods section of a manuscript.
These descriptions can be submitted via the Data Validator by selecting the ‘Documentation’ tab on the left side of the window. At present, you can’t see files after you’ve uploaded them. The data curation team will always look at file versions and date/time stamps and tak
Describe Mouse Model in MODEL-AD Tools Survey
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.
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.
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Email address for contact person
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Grant number
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Species
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Model Common Name
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Model URL (link to the stock number in the Jackson Lab database)
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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.
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.
Email address of the person submitting the survey
Grant number
Species
Model system name (see names in the AD Metadata Dictionary)
Model URL to Jax stock page (ex: https://www.jax.org/strain/031988)
Report card URL to 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 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
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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.
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.