Document toolboxDocument toolbox

Preparing and Contributing Study Documentation

Owned by Rich Yaxley (Unlicensed)
Last updated: Apr 30, 2024
2 min read

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 type

Naming Format

Number of Strains

Primary Screen

Site_PrimaryScreen

  • Jax.IU.Pitt_PrimaryScreen

  • UCI_PrimaryScreen

Many

Strain Validation

Site_StrainValidation

  • Jax.IU.Pitt_StrainValidation

  • UCI_StrainValidation

Many

Deep Phenotyping

Site_Model

  • Jax.IU.Pitt_APOE4_Trem2

  • UCI_5XFAD

Many

Pharmacokinetic

Site_Model_Drug

  • Jax.IU.Pitt_5XFAD_Verubecestat

One

Pilot Studies

  • Microbiome

  • Proteomics

  • Metabolomics

Site_StudyType_Pilot

Examples:

  • Jax.IU.Pitt.Proteomics_Metabolomics_Pilot

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.

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.

Methods Description

Each assay should include a brief description of the procedures, data collection, 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).