Difference between revisions of "PAMGO conference calls"

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'''GOC announcement: Regulation terms'''
'''GOC announcement: Regulation terms'''


"For some time now, the GO content developers have been aware that
                                      "For some time now, the GO content developers have been aware that
regulatory processes are not necessarily integral to the processes (as
                                        regulatory processes are not necessarily integral to the processes (as
previously indicated by the use of the 'part_of' relation) that they
                                        previously indicated by the use of the 'part_of' relation) that they
regulate. Nevertheless, regulatory processes have been represented as
                                        regulate. Nevertheless, regulatory processes have been represented as
part_of the processes they regulate. We have long intended to replace
                                        part_of the processes they regulate. We have long intended to replace
these part_of relationships with a new relationship type called
                                        these part_of relationships with a new relationship type called
'regulates'. We are now in a position to make this replacement"  
                                      'regulates'. We are now in a position to make this replacement"  
Entire e-mail attached. See  
                                        Entire e-mail attached. See  


'''Induction and Upregulation terms'''
'''Induction and Upregulation terms'''

Revision as of 13:27, 14 February 2008

PAMGO Conference Call-February 15 2008

Association files submitted to GOC: see ftp://ftp.geneontology.org/pub/go/gene-associations and AMIGO

      gene_association.PAMGO_Atumefaciens.gz
      gene_association.PAMGO_Oomycetes.gz

Update on association files for:

                 P. syringae
                 Erwinia
                 M. grisea


GOC announcement: Regulation terms

                                     "For some time now, the GO content developers have been aware that
                                       regulatory processes are not necessarily integral to the processes (as
                                       previously indicated by the use of the 'part_of' relation) that they
                                       regulate. Nevertheless, regulatory processes have been represented as
                                       part_of the processes they regulate. We have long intended to replace
                                       these part_of relationships with a new relationship type called
                                      'regulates'. We are now in a position to make this replacement" 
                                       Entire e-mail attached. See 

Induction and Upregulation terms

Induction and Upregulation of........ are currently child terms of positive regulation. Should this be merged into positive regulation?


Changing wording in some host terms

See wiki.............and make comments


Mini Reviews

Report

   Use of PAMGO terms by virulence community-Michelle


Others

PAMGO Conference Call-November 15 2007

Test set of annotations sent to Chris Mungall (GOC) File:PAMGO test assoc.xls

New "Properties" column in the association file

Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml New children codes under ISS (still under review)


Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree

See "PAMGO SUMMARY_2007" for Candace's proposal on this subject