Difference between revisions of "June 2012 - Weekly Pipeline Set-up"

Revision as of 16:00, 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.

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?

@@ Line 6: / Line 6: @@
 ***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.
 *Outstanding issues
 **dicty gene names
-***known issues: 'myosin' vs 'myosin IE'
+***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?