Uploading Animal Model Documentation
This article will teach you how to share new animal models with the AD Knowledge Portal’s Data Coordination Center (AD-DCC) at Sage Bionetworks.
MODEL-AD teams should inform the AD-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 Tools listed in the AD Knowledge Portal.
Animal Model Content
Each model should include a brief study description of how the animals were created and the key details listed below. The model details should match the information on the Jackson labs stock pages, and any discrepancies will need to be resolved.
Email address for contact person
Grant number
Species
Model Common Name
Model URL (link to the Jackson Lab model, eg, https://www.jax.org/strain/031988 )
Report card URL (link to the AlzForum model: https://www.alzforum.org/research-models/ )
Model description (<500 characters)
Targeted Genes
Background strain
Type (LOAD – Late Onset Alzheimer’s Disease, FAD – Familial Alzheimer’s Disease)
Create Model Entity in Experimental Tools
The AD-DCC will create a new entity in Synapse Experimental Tools. 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
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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 )
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