Difference between revisions of "June 2012 - Weekly Pipeline Set-up"
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***CCC verbs | ***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 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: [[http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/dicty/dicty_ccc.cgi]] | + | ***For an example, please see: [[http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/dicty/dicty_ccc.cgi dicty curation form]] |
*Outstanding issues | *Outstanding issues | ||
Revision as of 16:03, 26 June 2012
Goal: 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
