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  1. NIF
  2. NIF-11865

DISCO: import fly data from flymine

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    • Task
    • Resolution: Canceled
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    • NIF

    Description

      As an alternative to importing fly data from flybase, we can import it from flymine. This will also serve as a test for other intermine data sources.

      I've created a nice allele-phenotype query, here:
      http://www.flymine.org/release-36.1/service/query/results?query=%3Cquery+name%3D%22%22+model%3D%22genomic%22+view%3D%22Allele.primaryIdentifier+Allele.symbol+Allele.alleleClass+Allele.organism.name+Allele.gene.primaryIdentifier+Allele.gene.symbol+Allele.phenotypeAnnotations.annotationType+Allele.phenotypeAnnotations.description+Allele.phenotypeAnnotations.publications.pubMedId+Allele.phenotypeAnnotations.anatomyTerm.identifier+Allele.phenotypeAnnotations.anatomyTerm.name+Allele.phenotypeAnnotations.anatomyTerm.description+Allele.phenotypeAnnotations.developmentTerm.identifier+Allele.phenotypeAnnotations.developmentTerm.name+Allele.phenotypeAnnotations.developmentTerm.description+Allele.phenotypeAnnotations.cvTerms.identifier+Allele.phenotypeAnnotations.cvTerms.name+Allele.phenotypeAnnotations.cvTerms.description%22+longDescription%3D%22%22+sortOrder%3D%22Allele.primaryIdentifier+asc%22+constraintLogic%3D%22B+and+A%22%3E%3Cjoin+path%3D%22Allele.organism%22+style%3D%22OUTER%22%2F%3E%3Cjoin+path%3D%22Allele.phenotypeAnnotations.publications%22+style%3D%22OUTER%22%2F%3E%3Cjoin+path%3D%22Allele.phenotypeAnnotations.anatomyTerm%22+style%3D%22OUTER%22%2F%3E%3Cjoin+path%3D%22Allele.phenotypeAnnotations.cvTerms%22+style%3D%22OUTER%22%2F%3E%3Cjoin+path%3D%22Allele.phenotypeAnnotations.developmentTerm%22+style%3D%22OUTER%22%2F%3E%3Cconstraint+path%3D%22Allele.gene.symbol%22+code%3D%22B%22+op%3D%22%3D%22+value%3D%22fz%22%2F%3E%3Cconstraint+path%3D%22Allele.symbol%22+code%3D%22A%22+op%3D%22%3D%22+value%3D%22fz%5B3%5D%22%2F%3E%3C%2Fquery%3E&format=tab

      Or, as a perl script, see the attachment.
      It will make a allele-anatomy-stage-publication table, together with a few others.
      This will probably need to be transformed to get it to be proper EQ-style.

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            hoffmasc Scott Hoffmann
            nlw Nicole Washington
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              Updated:
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