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  1. NIF
  2. NIF-11676

Import IMPC phenotype data

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    • NIF
    • Issues closed as MONARCH has transitioned from UCSD services

    Description

      We need to fetch the IMPC data.
      This is the resource: http://neurolex.org/wiki/Category:Resource:IMPC
      ID: nlx_151660

      The phenotyping data can be fetched from their rest services. This could be in a script, or perhaps directly in the interop.

      http://wwwdev.ebi.ac.uk/mi/impc/dev/solr/genotype-phenotype/select?q=*:*&rows=10&wt=json

      see documentation here:
      https://github.com/mpi2/PhenotypeArchive/wiki/Genotype-associated-Phenotype-calls-REST-API

      i don't see anything in the documentation that will give all rows. i think we either need to fetch a very large number (in the above example, i used 10, but I've tried 10000 and it still worked), or iterate in groups (keying off the start parameter). it looks like there is presently 4886 annotations.

      'normality' of phenotypes is not captured in a rigorous way. you might have to map it. It's in the "category":"as described for wt". This is because they are showing legacy data from the europhenome project and they used different values for different phenotype tests to capture "normal". You can look up procedures here:
      https://www.mousephenotype.org/impress/pipelines

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              larawayb Bryan Laraway
              nlw Nicole Washington
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