galliaproject / gallia-genemania Goto Github PK

Note: This is only intended to showcase processing in Gallia, it is not complete nor thoroughly tested at the moment. Use output at your own risk.

See original announcement on the GeneMania google group and BioStars. For more information, see gallia-core documentation, in particular the bioinformatics examples section.

Uses Gallia transformations to turn TSV data from http://genemania.org/data/current/Homo_sapiens/ into objects like:

{
  "_id": "ENSG00000123456",

  "co_expression": [
    { "target": "ENSG00000654321",
      "context": [
        { "weight": 0.021,
          "network": "Meier-Seiler-2009",
          "source": "GEO",
          "pubmed": "12345678" },
        { "weight": 0.019,. .. },
        ...
  ],

  "predicted": [ ... ],
  ...  
}

Note that the processing makes use of Gallia's "poor man scaling", which can be seen in action here in the processing code.

• website: https://genemania.org/
• publication: "The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function"; Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q; Nucleic Acids Res. 2010 Jul 1;38 Suppl:W214-20 PubMed Abstract (PDF)

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