Contributing data to MPD

Much of the data in MPD are voluntarily contributed by investigators in the worldwide community. Projects can have one arm or two+ arm study designs, and MPD collects baseline characterizations, diet studies, drug and alcohol studies, treatment vs. control studies, aging and longevity studies, challenge / pathogen studies, and more. Data sets can be organized in various ways. If in doubt, simply contact us at an early stage: phenome@jax.org

What is submitted?

For phenotyping projects, we collect:
  • A data set, in Excel or tab-delimited format. It can be organized like either of these examples: Example 1 or Example 2.
  • Traits information. A list of the names, descriptions and units of the measured traits (often included as a tab in the above Excel file)
  • Investigators and directly-related publications
  • Funding or other acknowledgements
  • Other introductory content needed to understand and interpret the data
  • Send to phenome@jax.org

For other data types contact us at an early stage so we can work with you on specifics.

Must the data be part of a published paper?

Not a prerequisite, but encouraged. MPD release of your data can be delayed pending a publication (let us know in advance if this is your plan).

How are data sets reviewed and released?

Phenotyping projects are evaluated with respect to the recommendations below and other factors. Upon acceptance, we'll load your data into a password-protected area and let you know how to log in and preview it. You're free to send suggestions and feedback, and we'll work with you to polish your project. Finally, when you give us your OK, your data will be scheduled for public release.

Phenotype data recommendations

Strain nomenclature: Strain names should appear in the data set using current nomenclature. For unwieldy nomenclature, abbreviated names may be used in the data set. MPD staff will verify and resolve all strains to known vendor stock numbers and/or vendor urls.

Sexes: Females and males are segregated in all MPD data displays and analyses. Studies involving both sexes are preferred; studies of one sex are acceptable.

Unit of analysis: For strain survey data MPD's basic unit of analysis is strain / sex / measurement, for example: Peters1 platelet count mean for C57BL/6J females. For population studies unit of analysis is population / sex.

Required sample sizes: For strain survey data sets the number of animals tested ideally should be 10+ animals per analysis group (strain / sex). Smaller sample sizes are also acceptable. Many MPD data displays will warn when N < 5.

Number of strains tested: For strain survey data sets, the more strains studied, the better. At least 8-10 strains are required for many of the analyses, and projects involving less than 5 strains usually cannot be accessioned except as archives.

Animal IDs: Unique animal ID numbers should be present as a column in the data set.

Age at testing: For most purposes the target age range is 10-14 weeks, but any ages are acceptable. If animal age is uniform it may be conveyed as introductory content; if it varies the age values should be present as column(s) in the data set.

Protocol and Animal ocumentation: We will work with you to prepare a web-based protocol document describing workflow, methods, sampling considerations, any treatments applied, equipment, reagents, data collection, review, and analysis, and references. A separate brief animal information document (acquisition, environment and the like) is also typically prepared.