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Data downloads


Most files are available here: http://phenome.jax.org/download

We describe our various download offerings in more detail below.


    File     Description
measurements.csv Metadata for all phenotype measurements or traits in MPD. Includes descriptions, units, variable names, and so on. More info
datasets_metadata.xml An XML representation of data set titles and metadata, including descriptions, units, categorization, and ontology mappings of all public phenotype strain survey measurements / traits in MPD.  
ontology_mappings.csv Ontology term mappings for all individual MPD phenotype measurements / traits. 
straininfo.csv Strain name, vendor, stock number, and other attributes of each mouse strain with data in MPD. One row per strain. More info
datasets_strains.csv Indicates which mouse strains are involved in each data set, in a many-to-many mapping table.  
animaldatapoints.csv (zip) Contains one row per mouse phenotype data point for all individual mice tested. All public numeric MPD phenotype measurements are present except for data that were submitted as strain means. In this file strains are identified by MPD id number; join to straininfo (above) on mpd_strainid. More info
strainmeans.csv (zip) Strain averages and associated summary statistics for all numeric MPD phenotype measurements / traits. Contains one row per strain / sex / measurement. More info
categodata.csv Strain values for a handful of categorical (non-numeric) MPD phenotype measurements / traits. Contains one row per strain / sex / categorical measurement. More info
All strain means for a particular strain A download file of all phenotype strain means for a certain strain can be gotten from individual MPD strain pages... click here to search for a strain. Includes summary statistics and metadata as well.  
All strain means for a particular pair of strains A download file of all phenotype strain means for a certain pair of strains (for comparison) can be gotten from specific two-strain comparison pages. Includes summary statistics and metadata as well.  
measstats.csv (zip) Overall averages (all strains combined) for each MPD phenotype measurement. Includes associated summary statistics as well. More info
sexdiff.csv (zip) Sex differences (female vs. male) for each phenotype measurement and strain. More info
cc8pheno_table.csv Phenotype characterization (600+ traits) of the 8 Collaborative Cross founder strains extracted from phenotype data sets in MPD that involve 6 or more of them. Strain means and summary statistics, trait metadata optional. This file is available by request (phenome@jax.org).  
phenocorr.csv
Correlations between all pairwise combinations of numeric MPD pheno measurements. Pearson must be > |0.5| to be retained. Measurement pairs are correlated based on strain/sex means. Contains one row per eligible measurement pair / sex.     This file is available by request (phenome@jax.org). More info
gxmeascorr.csv
Contains one row for every eligible correlation between an MPD pheno measurement and a gene expression probeset. Segregated by sex. Eligibility for inclusion in table: Pearson |r|>0.5 and p value<0.005 and nstrains>=10.     This file is available by request (phenome@jax.org). More info

Phenotype strain survey project data sets
      • Find data sets
        Locate the project of interest. On the bottom of each project page
        is a place where individual data sets can be downloaded.
        Missing data codes

Genotype variation / SNP data
      • By ad hoc retrieval (any retrieval result can be downloaded)
      • By individual data set*
      • Strains with SNP data in MPD snpstrains.csv
      • Request that we create a data set for you
      • Field format of download files

      * except the very large data sets (usually available from supplying source).

Gene expression data sets
      • List data sets (most can be downloaded via GEO)

Phenotype strain survey data – mixtures of measurements
Build a download file made up of any combination of phenotype measurements. Locate phenotype data of interest, then click on the Tools icon in the left margin. Check the boxes for the measurements or traits you want then choose the Create your own data set tool.



If you'd like a data file that you don't see here we may be able to create it for you.
Send inquiries to phenome@jax.org



 




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