This grouping is for traits that are NOT expressions of genotype data (e.g. sex, weight, etc).

Phenotype traits are authenticated at the trait level, since there are no sub-groupings of them within a group.

The traits in this category are markers. Their sample data are the genotypes (encoded 1/0/1, though genotype probabilities could also be stored).

This data also exists in genotype files (in both .geno and BIMBAM formats). This data is stored in the database to allow for its use as cofactors when mapping.

The traits in this category are mRNA transcripts from locations in the genome. The sample data for these traits are expression values for the traits.

Individual datasets are from individual analyses, split by tissue.

This is a pseudo-grouping which costitutes of User-generated data. These have no real metadata. They are just lists of samples/strains (from a specific group) and values

The data for these is entered directly via the "Submit Trait" page or it is derived from the PCA traits generated from the "Correlation Matrix" page

This is the actual data for each sample.

A sample can be an individual, or the strain mean (average of multiple individuals)

The following are the expected "fields" for each instance of sample data:

• value: a numerical value. For "strain mean" items, it is the mean value.
• variance: variance for an individual and standard-error for "strain mean"
• ndata*/*num_cases: Number of samples for "strain mean" values. NIL for individuals (should probably be set to 1)

Sample data can have metadata, referred to as "Case Attributes". This is mostly non-numeric data e.g. sex, treatment type, etc.

• num_overlap: When doing correlations, it sets the number of overlapping samples for all target traits (number of samples where both the primary and target traits have values). This is not a true attribute, rather, it is a temporary attribute assigned to a trait "object".
• haveinfo: Get rid of this. An implementation detail. Indicates whether there was information found in the database for the given trait.
• mean: Average of all sample data values
• description_display*/*abbreviation: Phenotype description and abbreviated version (for display in figures or as a "trait symbol"). Depends on the authentication.

• name: PublishXRef ID. In GeneNetwork, it is a combination of a three-letter group code (InbredSet.InbredSetCode) and this ID makes up the displayed name
• lrs: Likelihood Ratio Statistic. In the code, this is the maximim QTL¹ association value when the trait in question is mapped using qtlreaper²
• LRS_location_repr: The location of the top QTL (above) as a printable string (chromosome + megabase location) e.g. "Chr2:20.019888"
• pvalue: P-value for the maximum QTL. There's a chance that the lrs score is derived from this. VERIFY!!!!!
• additive: additive effect³ for the maximum QTL
• pre_publication_description: Description of the phenotype before publication. Depending on the authentication, the pre_publication_description (which is not really human readable) is shown instead of the post_publication_description.
• post_publication_description: For published phenotypes, this is the description of the phenotype after publication.
• pubmed_id*/*pubmed_link*/*pubmed_text: For published phenotypes, these are the identifier, link to, and text of the publication on the PubMed⁴ site

• name: Transcript name
• location: Location of the mRNA transcript in the genome (chromosome + megabase location)
• lrs: Likelihood Ratio Statistic. In the code, this is the maximim QTL¹ association value when the trait in question is mapped using qtlreaper²
• LRS_location_repr: The location of the top QTL (above) as a printable string (chromosome + megabase location) e.g. "Chr2:20.019888"
• pvalue: P-value for the maximum QTL. There's a chance that the lrs score is derived from this. VERIFY!!!!!
• additive: additive effect³ for the maximum QTL
• symbol: gene symbol
• sequence: The DNA sequence
• probe_target_description*/*strand_probe*/*cell_id: VERIFY!!!!

• location: Location of the genetic marker