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Conversion Form

The Conversion Form allows you to convert from a selected input type to a selected output type. The input type will either be a coordinate system (based on centimorgans or basepairs) or a genetic feature ID which allows for RS numbers or gene names. When the input type is selected an example of the correct input text formatting will be shown as grayed text inside the input text box. If you have multiple values to convert you should separate each value with a newline. Also note that if your input data is already saved in a correctly formatted file on your computer you can just use the "Load Data From File" button. Once your data has been successfully converted you can save the results by clicking the "Download Conversion Results" button.

Refer to the following formatting rules for creating input data:
  • Use spaces or tabs to separate data columns
  • For SNP or Gene IDs the first column will be treated as the IDs and all subsequent columns will not be used for the conversion.
  • For centimorgan and basepair values the first column will be treated as a chromosome ID, the second column will be a cM or bp value and an optional third column will be a second cM or bp coordinate value. All columns after the third are ignored when converting data.

Here are some examples of correctly formatted input data:
  • Centimorgan input:
    1 44.4
    2 3.2234
    1 77
    5 44.21
    6 21.1
    4 19.002
    1 55
  • Centimorgan input with two value columns and an ignored fourth column:
    1 44.4      45      this
    2 3.2234    4       column
    1 77        80      will
    5 44.21     54.3    be
    6 21.1      41.14   ignored
  • Base pairs:
    1 92887845
    2 7821365
    1 172956646
    5 92572826
    6 47433029
    4 41364422
    1 131246731
  • SNP ID's:
    rs3675244
    rs3711314
    rs3023460
    rs3707114
    rs3706767


RESTful Service Interface

A RESTful web service interface is provided so that you can use the mouse map converter programmatically. In order to do this you need to send an HTTP POST to http://cgd.jax.org/mousemapconverter/resources/conversion/convert.json. In the header of the post you should have "Content-Type" and "Accept" both set to "application/json". The JSON object should be formatted as follows:
  • allowPerDataPointErrors (optional): if this is set to false or missing then errors that occur for any individual will not prevent the successful conversion of points that do not cause any error conditions.
  • fromUnits (optional): the units that we're converting to. This should be on of: "mm8", "GRCm38.p1", "maleShifmanMap", "femaleShifmanMap" or "averageShifmanMap". If this attribute is missing then we are converting from genotype feature IDs (such as RS#'s) rather than genome coordinates.
  • toUnits: the units that we're converting to. This should be on of: "mm8", "GRCm38.p1", "maleShifmanMap", "femaleShifmanMap" or "averageShifmanMap".
  • dataToConvert: an array of coordinates or genomic feature IDs to convert to "toUnits". If "fromUnits" is missing or null then this should be an array of strings, each of which will be treated as a genomic feature ID. Otherwise, if "fromUnits" is set, this is expected to be an array of arrays. For each of these arrays the first element will be a string chromosome ID and the remaining elements will be the numeric positions on that chromosome to convert.
The mouse map converter will respond with a JSON array of arrays, or in the case of an error a JSON object with an "errorMessage" property. This array of arrays is formatted just like "dataToConvert" where the first element is the chromosome ID and the remaining elements are all numeric positions. If the "allowPerDataPointErrors" property was set to true in the request then for those points where there was a conversion error there will be a JSON object with an "errorMessage" property in place of an array containing the conversion result.

Here is an example script written in python that shows how you can use this service to convert coordinates and check for error message in the result:

Please send questions or comments to mousemapconverter@jax.org

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