Cross Product Timeline

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Blessing of mature XP files

Mature xps currently live in scratch dir:

 cvs/go/scratch/xps
   biological_process_xp_cellular_component.obo
   biological_process_xp_cell.obo
 cvs/go/scratch/regulates_xp_live

We will officially bless these and move them out of scratch into

 go/ontology/editors/xps/

This will happen after the RO meeting (May 2008)

Note these will still be external to the main GO file. Editors or ontology consumers can optionally augment the GO with these xps.

Standard practice will be load both GO + xps at periodic intervals to perform QC etc

Integration of internal XPs (BP-CC, regulation) into main ontology file

This will happen after OE2 is released. Estimated time July 2008

Currently the internal xps live externally to the main GO file. Reasoner is run in batch and reports generated. It would be better to have this directly integrated.

Adding the xps directly into the main .obo file will mean the addition of intersection_of tags. These tags can be ignored by tools that do not require xps information - the graph will still be complete.

Example of augmented stanza:

 [Term]
 id: GO:0000122
 name: negative regulation of transcription from RNA polymerase II promoter
 namespace: biological_process
 def: "Any process that stops, prevents or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators]
 synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT []
 synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT []
 synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT []
 synonym: "inhibition of transcription from RNA polymerase II promoter" NARROW []
 synonym: "negative regulation of transcription from Pol II promoter" EXACT []
 is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter
 is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent
 intersection_of: GO:0065007 ! biological regulation
 intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter
 relationship: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter

Integration of CL XPs into edit cycle

Estimated time: September 2008

Note we will probably continue to maintain biological_process_xp_cell externally from the main gene_ontology*.obo files.

However, with OE2 it will become standard practice to load xps whenever the main GO file is to be edited, rather than periodically