June 2012 - Weekly Pipeline Set-up
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Jump to navigationJump to searchGoal: To set up a weekly CCC pipeline for dictyBase.
- Proposed workflow from Petra
- On a weekly basis:
- Monday - dictyBase will identify PDFs for curation
- Tuesday - Textpresso will process new PDFs, perform CCC search, and send source file output to CCC curation form on tazendra
- CCC curation performed by dictyBase curators will be stored on tazendra and exported to protein2go database at EBI (UniProt-GOA)
- We will use four Textpresso categories for the searches
- dicty gene
- CCC TAIR
- CCC assay terms
- CCC verbs
- For now, the source file format will be the same as what we used for the dicty searches for the BioCreative task.
- For an example, please see: dicty curation form
- On a weekly basis:
- Outstanding issues
- dicty gene names
- known issues: 'myosin' vs 'myosin IE - Petra's suggestion: remove 'myosin' from the gene list
- Greek characters in gene names - can this be addressed at all?
- dicty gene names