November 2012 - Weekly Pipeline Set-up

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Papers for Annotation

  • dictyBase (Bob) will send Textpresso PMIDs for CCC curation every Monday

Up-to-Date Gene Lists

  • dictyBase will send Textpresso the updated gene name, identifier, and synonym list every Monday night
  • we will need, in addition to the gene identifiers, names, and synonyms, the UniProtKB accessions in order to send the annotations to the Protein2GO tool
  • file format - does dictyBase produce a gpi for GO? See: http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Format

Results File to Curation Tool

  • Can we automate transfer of Textpresso search results from textpresso-dev to the appropriate directory on tazendra:

/home/acedb/kimberly/ccc_dicty/dicty_ccc_datafiles

Each file will need to be placed in a directory beginning with name 'results'

We should establish a naming convention for the files.

Transfer of Annotations to Protein2GO

  • Need User ID for WB
  • Will need to assign annotations using UniProtKB identifiers - via dictyBase gp2protein file or a gpi file?
  • Evidence code will be IDA (for now, future implementations will require IPI for complex annotations)
  • GO term identifier (already available in Dump Annotation File)
  • Reference identifier (probably PMID, available from Textpresso search)
  • Add Submit to Protein2GO button to CCC form


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