Phenotype2GO pipeline SOP

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Phenotype2GO pipeline (Combination of Sanger and Caltech):

The old Sanger script that generates the gene_association file (from Igor's work in January 2009) was changed:

  • Instead of excluding some papers while attaching GO terms to genes based on phenotypes from RNAi experiments (the so-called 'exclude list'), an 'include list' that comprises papers (mostly large scale genome-wide studies) is provided to the script. This list is curator approved and explicitly agreed upon for the propagation of GO terms to genes based on their RNAi phenotypes.
  • A new script is used, to use it invoke the script with the -includelist option, e.g.: Run -o gene_association.wb -rnai -include includelist.txt (this example only parses RNAi experiments, to generate full file, you should also give '-gene -var' options as before).
  • If you invoke it with '-acefile <filename>' option, the script will also generate Gene-GO_term connections derived from phenotypes. This is currently done by the phenotype procedure of the script.
  • This script: does not consult any exclusion/inclusion files
    • Follows a different logic from, this results in disparity between the gene_association file and the data that ends up in acedb.
    • So the phenotype procedure of needs to be disabled and the ace file generated by the new script needs to be used.
    • We do not want every gene with a phenotype to get a GO_term from the phenotype2GO mapping file, but just the genes from 'genome-wide' papers that have been reviewed.
    • To alter Sanger's version of, a patch file was provided.

Current status: From Igor's e-mail, March 2009: I don't think the phenotype option of the inherit_go_terms script has been disabled. The script should be run without the '-variation' option, but the gene_association file still has those. Try this: grep -i wbpheno gene_association.WS200.wb.ce |grep -v RNAi