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Status
colour Purple title TEAM Review

Study Naming

MODEL-AD data and metadata are organized by site and study. Studies are divided into directories by assay type, metadata, as well as a staging directory for data that has not yet been released. 

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Study type

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How many strains?

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Naming convention

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Example names

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Primary screen

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Many

Ready to contribute data to the AD Knowledge Portal?

1. Contact the https://sagebionetworks.jira.com/servicedesk/customer/portal/12
   Send a request to the AD + EL Service Desk to help add data or generate a publication dataset with a DOI.

2. Include MODEL-AD in the subject line

3. You will need the following information:

   1. Grant Number

   2. Contact PI

4. In order to configure the study in Synapse, please provide information about the following

   1. Study Name (see conventions below)

   2. Assays performed (see list of AD Metadata Dictionary)

   3. Data type

   4. File format

   5. Quantity of files, individual, and specimens

Study Name Conventions

MODEL-AD study names should be formatted as follows.

Study Documentation

Study Description

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Contributing Data Files to Synapse

Information about uploading and organizing data

Study Organization

Study directories will be organized like this:

• Study_Name/

  • Assay_a/

  • Assay_b/

  • Metadata/

  • Staging/ (private access)

File naming

File names must be unique and machine readable. Names can not include special characters. Furthermore, we recommend the names be concise and descriptive.

See general file naming recommendations from the Princeton U Library.

Study Documentation

Each study will need a Study Description, Methods Description, and Acknowledgment Statement. The Documentation Submission Form includes some templates for these documents and instructions about submitting the documents.

Study Description

MODEL-AD specific templates are being drafted and will be made available on Synapse (see Study, Acknowledgment, and Methods). Each study needs 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.

Issues to clarify include:

• Study and file naming conventions

• Study name abbreviation

• Descriptive study name

• Only include animal model

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Methods Description

Each assessment assay should be accompanied by include a brief description with information about of the assessment procedures, data generation and processingcollection, and analytical methods. This information is often described in the Materials and Methods section of a manuscript. This is a good opportunity to clarify or provide additional detail useful details that may not be included in the peer-reviewed manuscript.

Issues to clarify include:

• File naming conventions

• Assay-specific examples. Need a list of most common assays.

  • RNA sequencing

  • Behavioral

  • Frailty

  • Open field

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Acknowledgment Statement

Every MODEL-AD study should include the following acknowledgment:

The IU/JAX/PITT MODEL-AD Center was established with funding from The National Institute on Aging (U54 AG054345). Contact us: ModelAD@iupui.edu

The results published here are in whole or in part based on data obtained from the AD Knowledge Portal ( https://adknowledgeportal.synapse.org/ ). The IU/JAX/UCI MODEL-AD Center was established with funding from The National Institute on Aging (U54 AG054345-01 and AG054349). Aging studies are also supported by the Nathan Shock Center of Excellence in the Basic Biology of Aging (NIH P30 AG0380770).

Uploading Study and Assay Descriptions

These documents should be submitted to the dccvalidator to validate the variable keys and controlled vocabulary.

• Start by selecting the ‘Study Documentation’ tab on the left side of the window. 

• Please note, you will be unable see files after you’ve uploaded them. 

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