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Submitting MODEL-AD Experimental Tools

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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](https://docs.google.com/forms/d/e/1FAIpQLSfP0jZf_XZKP5Kqvf8GZbZgntCMAnAgDQww9e0jhsweqOYGqw/viewform). 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 following information. The model information should match that 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 Jax strain database)

  • Report card URL (link to the AlzForum)

  • Model description (<500 characters)

  • Targeted Genes

  • Background strain

  • Type (Late Onset AD, Familial AD)

Create Experimental Study in Experimental Tools

The Sage DCC creates a dummy folder in the AD Knowledge Portal’s [Experimental Tools file view](https://www.synapse.org/#!Synapse:syn22219740)

Annotate the Experimental Study

Sage DCC adds annotations to folders using the [file view](https://www.synapse.org/#!Synapse: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)

Link to Experimental Study

Sage DCC enters link to study with data available on the model.

Sage DCC writes release notes to inform the community a new model is available.

MODEL-AD teams provide mouse model reports

Mouse model information should be provided in a PDF. Sage DCC will link to this PDF to the mouse model card in Synapse.

Create Jira ticket and assigned to Director. Once approved this will be assigned to the governance team to set permissions accurately for files. Some files will be publicly viewable and will need approval by the governance team to be allowed. This occurs at the file, not 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

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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