Difference between revisions of "PAMGO conference calls"

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=='''PAMGO Conference Call-February 15 2008'''==
=='''PAMGO Conference Call-February 15 2008'''==


'''Association files submitted to GOC''': see ftp://ftp.geneontology.org/pub/go/gene-associations and AMIGO
''' update on association files submitted to GOC''':  
              
              
                 gene_association.PAMGO_Atumefaciens.gz
                 gene_association.PAMGO_Atumefaciens.gz
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                     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  
                     See entire e-mail:
                    Most of the modulation/regulation terms have a is_a relationship to parents
                    Few with part_of relationships, which  should still be fine if "part_of" is replaced with "regulates"
                    See examples:
 


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


                     Induction and Upregulation of........ are currently child terms of positive regulation. Should this be merged into positive
                     Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive
                     regulation?        
                     regulation? Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms   
                    anyway.
                    See examples:     




'''Changing wording in some host terms'''
'''Changing wording in some host terms'''


                     See wiki.............and make comments
                     Will put a list on the wiki soon for your comments




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'''Report'''
'''Report'''
                       Use of PAMGO terms by virulence community-Michelle
                       Use of PAMGO terms by virulence community-Michelle
'''PAMGO workshop July 14-16 2008'''
                      Please print out attached brochure and distribute at meetings/conferences you plan on attending before July
                      We need to attract a diverse group of people this year.





Revision as of 15:57, 14 February 2008

PAMGO Conference Call-February 15 2008

update on association files submitted to GOC:

               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" 
                   See entire e-mail: 
                   Most of the modulation/regulation terms have a is_a relationship to parents
                   Few with part_of relationships, which  should still be fine if "part_of" is replaced with "regulates"
                   See examples:


Induction and Upregulation terms

                    Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive
                    regulation?  Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms     
                    anyway.
                    See examples:      


Changing wording in some host terms

                    Will put a list on the wiki soon for your comments


Mini Reviews


Report

                      Use of PAMGO terms by virulence community-Michelle


PAMGO workshop July 14-16 2008

                     Please print out attached brochure and distribute at meetings/conferences you plan on attending before July
                     We need to attract a diverse group of people this year.


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