Difference between revisions of "November 2012 - Weekly Pipeline Set-up"
From WormBaseWiki
Jump to navigationJump to search (Created page with ''''Papers for Annotation''' *dictyBase (Bob) will send Textpresso PMIDs for CCC curation every Monday *dictyBase will send Textpresso the updated gene name, identifier, and synon…') |
|||
| (11 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
'''Papers for Annotation''' | '''Papers for Annotation''' | ||
*dictyBase (Bob) will send Textpresso PMIDs for CCC curation every Monday | *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 | *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 | ||
| + | |||
| + | |||
| + | |||
| + | Back to [[DictyBase]] | ||
Latest revision as of 17:10, 8 November 2012
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
Back to DictyBase
