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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. 

Study type

How many strains?

Naming convention

Example names

Primary screen

Many

Site_PrimaryScreen

  • Jax.IU.Pitt_PrimaryScreen

  • UCI_PrimaryScreen

Strain validation

Many

Site_StrainValidation

  • Jax.IU.Pitt_StrainValidation

  • UCI_StrainValidation

Deep phenotyping

One

Site_Strain

  • Jax.IU.Pitt_APOE4_Trem2

  • UCI_5XFAD

PK

One

Site_Strain_Drug

  • Jax.IU.Pitt_5XFAD_Verubecestat

Pilot Studies

  • Microbiome

  • Proteomics and Metabolomics

Many

Site_StudyType_Pilot

  • Jax.IU.Pitt_MicrobiomePilot Link

  • Jax.IU.Pitt.Proteomics_Metabolomics_Pilot Link

Study Documentation

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.

TODO A study description template will be created and made available here.

Issues to clarify include:

  • Study and file naming conventions

  • Study name abbreviation

  • Descriptive study name

  • Only include animal model

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.

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