Metadata Files
There are three types of metadata files for MODEL-AD:
individual animal metadata
biospecimen metadata
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
...
metadata
...
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.
...