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Detailed phenotype data set guidelines


Where do I send my data?
    Please send inquiries and data submissions to us at   phenome@jax.org


How do I know if my phenotype data set is a candidate for MPD?

What must be submitted?
    Names of investigators and project title. The principal/corresponding investigator should be listed first. (Example)

    Publications (optional) – citations for any directly related publications.

    A data set.

    If you're contributing a phenotype strain survey data set, then continue reading below. Otherwise, if you're contributing a gene expression strain survey data set or SNP data please contact us first at phenome@jax.org

    There are two options for supplying animal data for phenotype strain survey projects:

      Option A: A spreadsheet or text file where individual animals are shown as rows, and measurements are shown as columns. Each column must have a meaningful heading. For example:
      strainsexanimal_IDWBCRBCPLT...
      A/JfP014.369.191034...
      A/JfP024.309.241017...
      A/JfP034.389.151042...
      ... etc. ...
      A/JmP084.369.191034...
      A/JmP094.309.241017...
      A/JmP104.389.151042...
      ... etc. ...
      BALB/cByJfP234.369.191034...
      BALB/cByJfP244.309.241017...
      ... etc. ...

      Option B: A spreadsheet or text file having one row per animal measurement. This option is more verbose but sometimes easier to generate and manage. If this method is used, the data file should have these fields:

      ...
      strainsexanimal_IDparameter_nameparameter_value
      A/JfP01RBC9.19
      A/JfP02RBC9.24
      A/JfP03RBC9.15
      ... etc. ...
      A/JfP01WBC4.36
      A/JfP02WBC4.30
      A/JfP03WBC4.38
      ... etc. ...
      BALB/cByJfP23RBC9.19
      BALB/cByJfP24RBC9.24
      ... etc. ...
      Regardless of which option you use, check the MPD project recommendations for working parameters such number of strains to test and the number of animals per strain/sex that must be tested for reasonable statistical power. Individual animal data are greatly preferred over investigator-computed strain means. We'll compute strain means, SD, and other summary statistics using your individual animal values. Use of MPD missing data codes is recommended. Correct, current strain nomenclature is appreciated.

    A table of measurement descriptions and units. For example:
      varnamedescriptionunits
      WBCwhite blood cell countn/µL
      RBCred blood cell countn/µL
      PLTplatelet countn/µL
      This lets us know exactly what the values in the data set represent, and assists us in classifying your data into the MPD framework. There should be one row for each parameter in your data set.


    Information for the experimental protocol. If there's a pertinent publication given (as mentioned above) we will refer that first. Then we'll be in touch to gather necessary info, and we'll work to prepare an illustrated protocol document that you will have the chance to review. Here's an example illustrating of the types of information we typically gather.

    Animal documentation covering animal procurement, ages, environments, and diets. Same as protocol above... we will check publication and be in touch to gather necessary info, then we'll prepare animal documentation that you'll have the chance to review. Click here for an example.



How are submissions evaluated and curated?
    Data submissions are subject to preliminary scientific review and acceptance. We evaluate and prioritize incoming data sets based on these factors:
    • Is it complete and polished? Is the structure clear and concise?
    • Does it serve to characterize mouse strains in a straightforward way? Are there measurements that (when taken individually) serve to characterize strains?
    • Does it conform reasonably closely to the MPD project recommendations?
    • What's the perceived community interest level? How suitable is it to MPD's present needs?
    • Is it organized/formatted (see above) in a way that fits with the MPD structure/model?

    MPD's curatorial resources are limited, therefore timeframe may vary considerably. We may contact you to address structural issues, incomplete materials, or other problems. Status inquiries may be sent to phenome@jax.org . A data submission may be deprioritized if:
    • data do not seem to have been carefully reviewed or contain obvious errors or omissions
    • data do not serve to characterize mouse strains in a straightforward way or seem to require complex multivariate analyses in order to characterize strains.


    After passing preliminary review, we'll load your data into a password-protected area of the MPD and send you instructions on how to preview it. We'll work with you to finalize the project. When project materials are deemed complete and you notify us of your approval, your data will be made available to the public*.

    Contributing data is sometimes an iterative process. For long-term projects, you can submit data periodically as the project progresses. We can also update project attributes (such as names of investigators, related publications, etc.) upon notification at any time.

    Succinctness is important. Data sets should be structured to include fields that tell the story in the most concise way, so that the community can grasp and work with your data. If your data set includes additional "supporting" measurements, let us know so these can be stored in the data set but not represented as MPD measurements for display or correlations purposes.


* Important!
    Please do not use the MPD as a means to review and analyze data (such as to prepare a publication) without intending to release your data to the public within a reasonable amount of time. We reserve the right to automatically release data to the public 60 days after it is deemed complete if momentum towards release seems stalled.



 




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