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Metadata Files

There are three types of metadata files for MODEL-AD: 

  1. individual animal metadata

  2. biospecimen metadata

  3. assay metadata

Individual Metadata

This file contains metadata about each individual animal that is part of a study.  It includes information that is true of the animal as a whole:  individualID, genotype, room, litter, etc.  Each animal will have one row in the individual animal metadata template. In order for your metadata to validate successfully, please use the latest version of the MODEL-AD individual animal metadata template. 

Genotypes

The individual animal metadata template includes multiple variables to document genotype:

Variable

Definition

Example

officialName

Full name indicating all transgenes, taken from the strain’s Jax datasheet

B6.Cg-Apoetm1.1(APOE*4)Adiuj Abca7em2Adiuj Trem2em1Adiuj/J

modelSystemName

Strain annotation, based on the MODEL-AD strain table

Abca7A1527GSNP (used as the annotation)

modelCommonName

Strain name that includes LOAD1 or LOAD2 terminology

LOAD1.Abca7-KI

stockNumber

The Jax stock number, if available

030283

genotypeBackground

Background genotype

C57BL6J

genotype

Genotype of animal that indicates littermate carriers vs noncarriers

Abca7_KI_homozygous OR Abca7_KI_noncarrier


Biospecimen Metadata

A biospecimen is a sample of cells, tissue, RNA, DNA, etc.  The biospecimen metadata file contains information about each biospecimen that is part of a study, including things like what organ and tissue the specimen is from, the weight of the specimen, etc.  Please see the biospecimen metadata template for a current template to work with.

The biospecimen metadata file is linked to the individual animal metadata file by the ‘individualID’ variable, which appears in both files.  The individualID variable should be consistent across these two files.  Each individualID may have more than one associated specimenID.  Note that not all data will have an associated biospecimen – things like behavioral studies or imaging may only have records in the individual animal metadata file.

The biospecimen metadata file is also related to the assay metadata file(s) by the ‘specimenID’ value, which appears in both (all) files.  The specimenID variable should be consistent across these two files.  If more than one assay was conducted on the same specimen, the same specimenID should be used throughout. 

Assay Metadata

This file contains metadata about each assay for which data is provided.  There are multiple assay metadata templates, since the information collected will vary by assay.  See the ‘Templates and Upload Conventions’ section for links to all available metadata templates.

The assay metadata file is linked to the biospecimen metadata file by the ‘specimenID’ variable, which appears in both files.  The specimenID variable should be consistent across these two files.

Note that not all assays have related assay metadata files.  

Image Added

Here’s a graphical representation of the relationship between individualID and specimenID across the different metadata files.  IndividualID should be consistent across the individual animal and biospecimen metadata templates.  SpecimenID should be consistent between the biospecimen and assay metadata files.