Versions Compared

Old Version 9

changes.mady.by.user Rich Yaxley

Saved on

compared with

New Version 10

changes.mady.by.user Rich Yaxley

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Info

Status
colourPurple
titleTEAM Review
All teams should review and agree on study conventions.

Table of Contents

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_StrainModel

  • Jax.IU.Pitt_APOE4_Trem2

  • UCI_5XFAD

Pharmacokinetic (PK)

One

Site_StrainModel_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

...

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.

Status
colourBlue
titleTODO
A Download the 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

...

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.

...

  • 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.

...