November 2012 - Weekly Pipeline Set-up
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- 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 Gene Product Data File: 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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