TEAM REVIEW All teams should review and agree on study conventions.
Study Naming
MODEL-AD data and metadata are organized by site and study.
Study type | How many strains? | Naming convention | Example names |
Primary screen | Many | Site_PrimaryScreen |
|
Strain validation | Many | Site_StrainValidation |
|
Deep phenotyping | One | Site_Model |
|
Pharmacokinetic (PK) | One | Site_Model_Drug |
|
Pilot Studies
| Many | Site_StudyType_Pilot |
MODEL-AD Studies are usually organized with directories as follows:
Study_name/
Assay_Type_1/
(data from first assay)Assay_Type_2/
(data from second assay)Metadata/
Staging/
(data that has yet to be released)Assay_Type_n/
(unreleased data from nth assay)
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.
Download the study description template.
Assay Description
Each assessment should be accompanied by a brief description with information about the assessment procedures, data generation and processing, 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 that may not be included in the peer-reviewed manuscript.
TODO A methods description template will be made available here.
Issues to clarify include:
File naming conventions
Assay-specific examples. Need a list of most common assays.
RNA sequencing
Behavioral
Frailty
Open field
Acknowledgement Statement
Every MODEL-AD study should include the following acknowledgment:
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.
TODO Describe the process for using the dccvalidator.
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.
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 version.
Add Comment