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Study Naming
MODEL-AD data and metadata are organized by site and study. Studies are divided into subfolders by assay type, plus a subfolder for all study metadata and a staging folder 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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Ready to contribute data to the AD Knowledge Portal?
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.Include
MODEL-ADin the subject lineYou will need the following information:
Grant Number
Contact PI
In order to configure the study in Synapse, please provide information about the following
Study Name (see conventions below)
Assays performed (see list of AD Metadata Dictionary)
Data type
File format
Quantity of files, individual, and specimens
Study Name Conventions
MODEL-AD study names should be formatted as follows.
Study type | Naming Format | Number of Strains |
Primary Screen |
| Many |
Strain |
Validation |
| Many |
Deep |
Phenotyping |
One
|
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Many |
Pharmacokinetic |
|
| One | |
Pilot Studies
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Examples:
| Many |
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.Each study should be accompanied by
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.
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Methods Description
Each assay should be accompanied by include a short description that includes specimen processingbrief description of the procedures, 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 take the most recent version of the file, so if in doubt, please feel free to upload a new versioncollection, and analytical methods. This is a good opportunity to provide useful details that may not be included in the manuscript.
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).